Starting phenix.real_space_refine
on Thu Jul 31 20:24:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iqg_35661/07_2025/8iqg_35661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iqg_35661/07_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_35661/07_2025/8iqg_35661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iqg_35661/07_2025/8iqg_35661.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iqg_35661/07_2025/8iqg_35661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iqg_35661/07_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-5711/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: 5.25, per 1000 atoms: 0.62
  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: 2.08
  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: 0.96
  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: 2.27

  Time building geometry restraints manager: 2.47 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:             0.920
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.220
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.530
-------------------------------------------------------------------------------
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  : 0.999 
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: 0.2506
  time to fit residues: 61.7207
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  : 1.046 
-------------------------------------------------------------------------------
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 = 0.3635 r_free = 0.3635 target = 0.086984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.065696 restraints weight = 29106.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.068342 restraints weight = 15912.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.070097 restraints weight = 11200.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
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  : 1.071 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7744 (tp-100)
REVERT: A  576 LYS cc_start: 0.8962 (mttt) cc_final: 0.8580 (tttm)
REVERT: A  685 LYS cc_start: 0.8750 (tmtt) cc_final: 0.8384 (ttmm)
REVERT: A  702 LYS cc_start: 0.9255 (ptmm) cc_final: 0.8474 (ptmm)
REVERT: D   73 GLU cc_start: 0.8646 (pt0) cc_final: 0.8334 (pt0)
REVERT: D   93 GLN cc_start: 0.8824 (tt0) cc_final: 0.8610 (tt0)
REVERT: E   95 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8438 (mtp85)
REVERT: C   36 MET cc_start: 0.8391 (ttm) cc_final: 0.8161 (ttt)
REVERT: C  154 TYR cc_start: 0.8953 (p90) cc_final: 0.8662 (p90)
REVERT: C  253 MET cc_start: 0.8417 (mpp) cc_final: 0.7870 (mpp)
REVERT: C  342 LEU cc_start: 0.9406 (tp) cc_final: 0.9138 (tt)
REVERT: C  365 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8197 (mt-10)
REVERT: C  394 SER cc_start: 0.9551 (OUTLIER) cc_final: 0.9159 (t)
REVERT: B   18 SER cc_start: 0.9379 (t) cc_final: 0.8830 (p)
REVERT: B   20 ASP cc_start: 0.8658 (t0) cc_final: 0.8225 (t0)
REVERT: B   40 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8268 (p0)
REVERT: B   47 GLU cc_start: 0.8629 (pm20) cc_final: 0.7337 (pm20)
REVERT: B  185 TYR cc_start: 0.9097 (m-10) cc_final: 0.8855 (m-10)
REVERT: B  189 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7677 (tp)
REVERT: B  267 TYR cc_start: 0.9060 (m-80) cc_final: 0.8714 (m-80)
REVERT: B  324 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8291 (mp0)
REVERT: B  369 TYR cc_start: 0.8015 (m-80) cc_final: 0.7644 (m-80)
  outliers start: 33
  outliers final: 7
  residues processed: 178
  average time/residue: 0.2113
  time to fit residues: 51.3032
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  : 0.950 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 85 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3593 r_free = 0.3593 target = 0.084020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.063545 restraints weight = 30142.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.066075 restraints weight = 16063.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.067760 restraints weight = 11165.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8717  Z= 0.205
  Angle     :  0.624  11.602  11893  Z= 0.309
  Chirality :  0.045   0.174   1360
  Planarity :  0.004   0.054   1536
  Dihedral  :  4.210  37.141   1249
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 27.19 %
    Favored  : 68.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.08 (0.25), residues: 1150
  helix:  1.48 (0.36), residues: 213
  sheet: -1.62 (0.29), residues: 313
  loop : -0.95 (0.24), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 185 
 HIS   0.005   0.001   HIS C 226 
 PHE   0.013   0.001   PHE C  61 
 TYR   0.010   0.001   TYR C 409 
 ARG   0.008   0.001   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03518 (  261)
  hydrogen bonds       : angle       5.26374 (  729)
  covalent geometry    : bond        0.00462 ( 8717)
  covalent geometry    : angle       0.62390 (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
  163 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7600 (tp-100)
REVERT: A  576 LYS cc_start: 0.9028 (mttt) cc_final: 0.8562 (tttt)
REVERT: A  685 LYS cc_start: 0.8626 (tmtt) cc_final: 0.8290 (ttmm)
REVERT: A  700 ASP cc_start: 0.7396 (p0) cc_final: 0.7134 (p0)
REVERT: D   73 GLU cc_start: 0.8744 (pt0) cc_final: 0.8454 (pt0)
REVERT: E   53 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8822 (tp30)
REVERT: C   36 MET cc_start: 0.8566 (ttm) cc_final: 0.8353 (ttt)
REVERT: C  342 LEU cc_start: 0.9411 (tp) cc_final: 0.9175 (tt)
REVERT: C  365 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8234 (mt-10)
REVERT: C  394 SER cc_start: 0.9705 (OUTLIER) cc_final: 0.9259 (t)
REVERT: B   18 SER cc_start: 0.9370 (t) cc_final: 0.8994 (p)
REVERT: B   20 ASP cc_start: 0.8663 (t0) cc_final: 0.8178 (t0)
REVERT: B  324 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8404 (mt-10)
  outliers start: 31
  outliers final: 14
  residues processed: 153
  average time/residue: 0.2191
  time to fit residues: 45.7575
Evaluate side-chains
  133 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  108 ASN
Chi-restraints excluded: chain E residue   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 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:    2.9990
   chunk 112 optimal weight:   10.0000
   chunk 28 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 15 optimal weight:    7.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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**
B  30 HIS
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  65 HIS
B  70 ASN
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.085319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.064771 restraints weight = 29762.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.067357 restraints weight = 16024.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.069084 restraints weight = 11176.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2557

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= 0.126
  Angle     :  0.599  11.483  11893  Z= 0.295
  Chirality :  0.045   0.221   1360
  Planarity :  0.004   0.038   1536
  Dihedral  :  3.994  19.404   1247
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 28.35 %
    Favored  : 68.69 %
  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:  1.52 (0.36), residues: 214
  sheet: -1.65 (0.28), residues: 318
  loop : -0.90 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 255 
 HIS   0.006   0.001   HIS B  65 
 PHE   0.017   0.001   PHE A 508 
 TYR   0.015   0.001   TYR C 154 
 ARG   0.007   0.001   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03191 (  261)
  hydrogen bonds       : angle       4.95660 (  729)
  covalent geometry    : bond        0.00286 ( 8717)
  covalent geometry    : angle       0.59922 (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
  157 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  512 LEU cc_start: 0.7707 (mt) cc_final: 0.7501 (mt)
REVERT: A  516 GLN cc_start: 0.7935 (tp-100) cc_final: 0.7590 (tp-100)
REVERT: A  576 LYS cc_start: 0.9026 (mttt) cc_final: 0.8576 (tttt)
REVERT: A  685 LYS cc_start: 0.8696 (tmtt) cc_final: 0.8328 (ttmm)
REVERT: D   73 GLU cc_start: 0.8734 (pt0) cc_final: 0.8387 (pt0)
REVERT: E   53 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8645 (tp30)
REVERT: C  253 MET cc_start: 0.8334 (mpp) cc_final: 0.7676 (mpp)
REVERT: C  324 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8778 (mm-40)
REVERT: C  365 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8185 (mt-10)
REVERT: B   14 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8718 (mt-10)
REVERT: B   18 SER cc_start: 0.9358 (t) cc_final: 0.9015 (p)
REVERT: B   20 ASP cc_start: 0.8589 (t0) cc_final: 0.8224 (t0)
REVERT: B  235 SER cc_start: 0.9261 (OUTLIER) cc_final: 0.8868 (p)
REVERT: B  324 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8351 (mt-10)
REVERT: B  351 ASP cc_start: 0.8339 (t0) cc_final: 0.7786 (m-30)
  outliers start: 23
  outliers final: 12
  residues processed: 147
  average time/residue: 0.2157
  time to fit residues: 43.4562
Evaluate side-chains
  134 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
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   30 THR
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  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  235 SER
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:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0270
   chunk 107 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 104 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.9242

-------------------------------------------------------------------------------
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 328 HIS
B  30 HIS
B  65 HIS
B  70 ASN
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.085178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.064701 restraints weight = 29846.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.067217 restraints weight = 16786.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.068859 restraints weight = 11994.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2770

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= 0.128
  Angle     :  0.593  12.668  11893  Z= 0.288
  Chirality :  0.045   0.178   1360
  Planarity :  0.004   0.035   1536
  Dihedral  :  3.914  19.604   1247
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 27.71 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.25), residues: 1150
  helix:  1.62 (0.36), residues: 213
  sheet: -1.64 (0.27), residues: 318
  loop : -0.86 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 402 
 HIS   0.010   0.001   HIS C 176 
 PHE   0.011   0.001   PHE A 508 
 TYR   0.009   0.001   TYR C 409 
 ARG   0.006   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02962 (  261)
  hydrogen bonds       : angle       4.80255 (  729)
  covalent geometry    : bond        0.00297 ( 8717)
  covalent geometry    : angle       0.59286 (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: 34
    poor density    : 134
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7557 (tp-100)
REVERT: A  685 LYS cc_start: 0.8716 (tmtt) cc_final: 0.8321 (ttmm)
REVERT: D   73 GLU cc_start: 0.8757 (pt0) cc_final: 0.8411 (pt0)
REVERT: E   40 ARG cc_start: 0.8997 (ptt-90) cc_final: 0.8617 (ptt-90)
REVERT: E   53 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8650 (tp30)
REVERT: E   95 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8341 (mtp85)
REVERT: C   15 ARG cc_start: 0.8652 (tpm170) cc_final: 0.8397 (tpm170)
REVERT: C  203 CYS cc_start: 0.8370 (m) cc_final: 0.8020 (m)
REVERT: C  253 MET cc_start: 0.8308 (mpp) cc_final: 0.7582 (mpp)
REVERT: C  324 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8744 (mm-40)
REVERT: C  365 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8159 (mt-10)
REVERT: C  399 MET cc_start: 0.8659 (tmm) cc_final: 0.8434 (tmm)
REVERT: C  406 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7901 (tm-30)
REVERT: B   14 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8725 (mt-10)
REVERT: B   18 SER cc_start: 0.9353 (t) cc_final: 0.8876 (m)
REVERT: B   20 ASP cc_start: 0.8598 (t0) cc_final: 0.8204 (t0)
REVERT: B   70 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8056 (m-40)
REVERT: B  133 TYR cc_start: 0.8294 (m-10) cc_final: 0.8037 (m-10)
REVERT: B  324 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8329 (mt-10)
REVERT: B  351 ASP cc_start: 0.8342 (t0) cc_final: 0.7796 (m-30)
  outliers start: 34
  outliers final: 23
  residues processed: 153
  average time/residue: 0.2111
  time to fit residues: 43.9589
Evaluate side-chains
  144 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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  701 LEU
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 E residue   95 ARG
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  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   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:    0.6980
   chunk 54 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   chunk 68 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    1.0584

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.085305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.064964 restraints weight = 29785.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.067457 restraints weight = 16644.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.069143 restraints weight = 11860.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2922

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= 0.136
  Angle     :  0.598  11.229  11893  Z= 0.289
  Chirality :  0.045   0.179   1360
  Planarity :  0.004   0.034   1536
  Dihedral  :  3.921  19.483   1247
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 27.58 %
    Favored  : 68.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.94 (0.24), residues: 1150
  helix:  1.70 (0.36), residues: 213
  sheet: -1.62 (0.27), residues: 318
  loop : -0.84 (0.24), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 402 
 HIS   0.012   0.001   HIS C 176 
 PHE   0.012   0.001   PHE A 508 
 TYR   0.010   0.001   TYR C 154 
 ARG   0.008   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02879 (  261)
  hydrogen bonds       : angle       4.77820 (  729)
  covalent geometry    : bond        0.00313 ( 8717)
  covalent geometry    : angle       0.59781 (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: 32
    poor density    : 131
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7558 (tp-100)
REVERT: A  685 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8370 (ttmm)
REVERT: D   73 GLU cc_start: 0.8782 (pt0) cc_final: 0.8539 (pt0)
REVERT: E   40 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8614 (ptt-90)
REVERT: E   53 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8635 (tp30)
REVERT: E   95 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8317 (mtp85)
REVERT: C  203 CYS cc_start: 0.8355 (m) cc_final: 0.8153 (m)
REVERT: C  253 MET cc_start: 0.8311 (mpp) cc_final: 0.7504 (mpp)
REVERT: C  324 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8741 (mm-40)
REVERT: C  365 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8166 (mt-10)
REVERT: B   14 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8742 (mt-10)
REVERT: B   18 SER cc_start: 0.9329 (t) cc_final: 0.8877 (m)
REVERT: B   20 ASP cc_start: 0.8603 (t0) cc_final: 0.8195 (t0)
REVERT: B   70 ASN cc_start: 0.8859 (m110) cc_final: 0.8470 (m-40)
REVERT: B  324 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8310 (mt-10)
  outliers start: 32
  outliers final: 20
  residues processed: 148
  average time/residue: 0.2023
  time to fit residues: 41.8846
Evaluate side-chains
  138 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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  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   92 LEU
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   40 ARG
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:    0.0050
   chunk 112 optimal weight:   10.0000
   chunk 101 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 88 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 72 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   overall best weight:    1.9398

-------------------------------------------------------------------------------
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  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 HIS
B  65 HIS
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.083447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.062907 restraints weight = 29950.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.065306 restraints weight = 17065.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.066900 restraints weight = 12329.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.3039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   8717  Z= 0.200
  Angle     :  0.612  11.080  11893  Z= 0.302
  Chirality :  0.045   0.184   1360
  Planarity :  0.004   0.034   1536
  Dihedral  :  4.025  19.692   1247
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 28.35 %
    Favored  : 67.40 %
  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: -1.03 (0.24), residues: 1150
  helix:  1.47 (0.36), residues: 220
  sheet: -1.56 (0.27), residues: 317
  loop : -0.93 (0.24), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 402 
 HIS   0.010   0.001   HIS C 176 
 PHE   0.012   0.001   PHE D  78 
 TYR   0.009   0.001   TYR C 409 
 ARG   0.006   0.000   ARG C  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03006 (  261)
  hydrogen bonds       : angle       4.84968 (  729)
  covalent geometry    : bond        0.00450 ( 8717)
  covalent geometry    : angle       0.61152 (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
  153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7534 (tp-100)
REVERT: D   73 GLU cc_start: 0.8825 (pt0) cc_final: 0.8435 (pt0)
REVERT: E   40 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8611 (ptp-170)
REVERT: E   53 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8638 (tp30)
REVERT: E   95 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8277 (mtp85)
REVERT: E  100 PHE cc_start: 0.8983 (m-80) cc_final: 0.8651 (m-80)
REVERT: C  324 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8754 (mm-40)
REVERT: C  365 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8175 (mt-10)
REVERT: B   18 SER cc_start: 0.9325 (t) cc_final: 0.8870 (m)
REVERT: B   20 ASP cc_start: 0.8605 (t0) cc_final: 0.8206 (t0)
REVERT: B   70 ASN cc_start: 0.8955 (m110) cc_final: 0.8429 (m-40)
REVERT: B  324 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8312 (mt-10)
REVERT: B  351 ASP cc_start: 0.8329 (t0) cc_final: 0.7750 (m-30)
  outliers start: 33
  outliers final: 20
  residues processed: 140
  average time/residue: 0.2073
  time to fit residues: 40.4802
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  : 1.103 
-------------------------------------------------------------------------------
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  689 VAL
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   40 ARG
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue   95 ARG
Chi-restraints excluded: chain C residue   53 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  176 HIS
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 57 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 20 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0770
   chunk 77 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.6538

-------------------------------------------------------------------------------
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**
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 = 0.3701 r_free = 0.3701 target = 0.086836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.067141 restraints weight = 29848.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.069709 restraints weight = 15949.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.071420 restraints weight = 11085.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3229

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= 0.116
  Angle     :  0.610  11.505  11893  Z= 0.295
  Chirality :  0.045   0.195   1360
  Planarity :  0.004   0.034   1536
  Dihedral  :  3.961  19.731   1247
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 29.12 %
    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:  1.62 (0.36), residues: 214
  sheet: -1.52 (0.27), residues: 329
  loop : -0.79 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 255 
 HIS   0.017   0.001   HIS C 176 
 PHE   0.013   0.001   PHE A 508 
 TYR   0.008   0.001   TYR B 267 
 ARG   0.007   0.000   ARG A 556 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02876 (  261)
  hydrogen bonds       : angle       4.73712 (  729)
  covalent geometry    : bond        0.00273 ( 8717)
  covalent geometry    : angle       0.60988 (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
  153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7932 (tp-100) cc_final: 0.7538 (tp-100)
REVERT: A  575 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8243 (m-40)
REVERT: A  685 LYS cc_start: 0.8891 (tmmt) cc_final: 0.8383 (ttmm)
REVERT: D   73 GLU cc_start: 0.8802 (pt0) cc_final: 0.8428 (pt0)
REVERT: E   53 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8498 (tp30)
REVERT: E   95 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8256 (mtp85)
REVERT: E  100 PHE cc_start: 0.9011 (m-80) cc_final: 0.8714 (m-80)
REVERT: C  253 MET cc_start: 0.8307 (mpp) cc_final: 0.7541 (mpp)
REVERT: C  365 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8122 (mt-10)
REVERT: C  406 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7872 (tm-30)
REVERT: B   18 SER cc_start: 0.9299 (t) cc_final: 0.8874 (m)
REVERT: B   20 ASP cc_start: 0.8565 (t0) cc_final: 0.8192 (t0)
REVERT: B   42 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7533 (mmt90)
REVERT: B   45 LYS cc_start: 0.9141 (mtpp) cc_final: 0.8518 (mtmt)
REVERT: B   70 ASN cc_start: 0.8854 (m110) cc_final: 0.8462 (m-40)
REVERT: B  229 HIS cc_start: 0.8544 (m-70) cc_final: 0.8158 (m-70)
REVERT: B  324 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8247 (mp0)
REVERT: B  351 ASP cc_start: 0.8335 (t0) cc_final: 0.7706 (m-30)
  outliers start: 30
  outliers final: 21
  residues processed: 143
  average time/residue: 0.2139
  time to fit residues: 42.0832
Evaluate side-chains
  143 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
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  575 ASN
Chi-restraints excluded: chain A residue  619 ASP
Chi-restraints excluded: chain A residue  689 VAL
Chi-restraints excluded: chain A residue  701 LEU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain 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  310 LEU
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain B residue   42 ARG
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  318 VAL
Chi-restraints excluded: chain B residue  335 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 79 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 112 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0980
   chunk 33 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.9386

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.085915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.065333 restraints weight = 29903.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.067893 restraints weight = 16570.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.069596 restraints weight = 11762.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.3293

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= 0.131
  Angle     :  0.620  12.013  11893  Z= 0.302
  Chirality :  0.046   0.244   1360
  Planarity :  0.004   0.060   1536
  Dihedral  :  3.933  19.622   1247
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 29.38 %
    Favored  : 67.40 %
  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: -0.94 (0.24), residues: 1150
  helix:  1.47 (0.36), residues: 221
  sheet: -1.44 (0.27), residues: 322
  loop : -0.89 (0.24), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 402 
 HIS   0.015   0.001   HIS C 176 
 PHE   0.020   0.001   PHE B 237 
 TYR   0.008   0.001   TYR C 409 
 ARG   0.008   0.000   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02936 (  261)
  hydrogen bonds       : angle       4.74232 (  729)
  covalent geometry    : bond        0.00305 ( 8717)
  covalent geometry    : angle       0.62035 (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
  148 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7498 (tp-100)
REVERT: A  685 LYS cc_start: 0.8927 (tmmt) cc_final: 0.8394 (ttmm)
REVERT: A  699 ASP cc_start: 0.8030 (p0) cc_final: 0.7808 (p0)
REVERT: A  700 ASP cc_start: 0.7616 (p0) cc_final: 0.7331 (p0)
REVERT: D    5 GLN cc_start: 0.6841 (pm20) cc_final: 0.5568 (pm20)
REVERT: D   73 GLU cc_start: 0.8754 (pt0) cc_final: 0.8398 (pt0)
REVERT: E   36 ARG cc_start: 0.9013 (ptp-170) cc_final: 0.8401 (ptp90)
REVERT: E   53 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8469 (tp30)
REVERT: E   95 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8280 (mtp85)
REVERT: E  100 PHE cc_start: 0.9021 (m-80) cc_final: 0.8717 (m-80)
REVERT: C  253 MET cc_start: 0.8281 (mpp) cc_final: 0.7529 (mpp)
REVERT: C  352 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7677 (tp30)
REVERT: C  365 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8115 (mt-10)
REVERT: B   18 SER cc_start: 0.9282 (t) cc_final: 0.8849 (m)
REVERT: B   20 ASP cc_start: 0.8555 (t0) cc_final: 0.8204 (t0)
REVERT: B   70 ASN cc_start: 0.8769 (m110) cc_final: 0.8402 (m-40)
REVERT: B  229 HIS cc_start: 0.8553 (m-70) cc_final: 0.8196 (m-70)
REVERT: B  299 GLU cc_start: 0.8776 (tp30) cc_final: 0.8526 (tm-30)
REVERT: B  324 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8266 (mp0)
REVERT: B  351 ASP cc_start: 0.8314 (t0) cc_final: 0.7667 (m-30)
  outliers start: 25
  outliers final: 18
  residues processed: 140
  average time/residue: 0.2240
  time to fit residues: 42.6721
Evaluate side-chains
  133 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
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   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  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  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:    0.7980
   chunk 60 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 53 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 HIS
B  65 HIS
B  70 ASN
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.087355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.065840 restraints weight = 29507.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.068470 restraints weight = 16400.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.070089 restraints weight = 11709.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8717  Z= 0.125
  Angle     :  0.640  14.382  11893  Z= 0.310
  Chirality :  0.046   0.212   1360
  Planarity :  0.004   0.034   1536
  Dihedral  :  3.916  19.616   1247
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 29.64 %
    Favored  : 67.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.86 (0.24), residues: 1150
  helix:  1.67 (0.36), residues: 216
  sheet: -1.37 (0.27), residues: 322
  loop : -0.88 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 402 
 HIS   0.013   0.001   HIS C 176 
 PHE   0.017   0.001   PHE B 237 
 TYR   0.010   0.001   TYR C 409 
 ARG   0.007   0.000   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02922 (  261)
  hydrogen bonds       : angle       4.75536 (  729)
  covalent geometry    : bond        0.00290 ( 8717)
  covalent geometry    : angle       0.63996 (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
  137 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7607 (tp-100)
REVERT: A  519 ARG cc_start: 0.8710 (mtm110) cc_final: 0.8088 (ttp-110)
REVERT: A  685 LYS cc_start: 0.8936 (tmmt) cc_final: 0.8383 (ttmm)
REVERT: A  699 ASP cc_start: 0.7999 (p0) cc_final: 0.7756 (p0)
REVERT: A  700 ASP cc_start: 0.7598 (p0) cc_final: 0.7311 (p0)
REVERT: D   73 GLU cc_start: 0.8782 (pt0) cc_final: 0.8420 (pt0)
REVERT: E   36 ARG cc_start: 0.9070 (ptp-170) cc_final: 0.8426 (ptp90)
REVERT: E   53 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8466 (tp30)
REVERT: E   78 ARG cc_start: 0.8524 (mtp180) cc_final: 0.7976 (ptm-80)
REVERT: E  100 PHE cc_start: 0.9048 (m-80) cc_final: 0.8695 (m-80)
REVERT: C  253 MET cc_start: 0.8308 (mpp) cc_final: 0.7493 (mpp)
REVERT: C  365 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8133 (mt-10)
REVERT: B   14 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8670 (mt-10)
REVERT: B   18 SER cc_start: 0.9298 (t) cc_final: 0.8854 (m)
REVERT: B   20 ASP cc_start: 0.8582 (t0) cc_final: 0.8203 (t0)
REVERT: B   70 ASN cc_start: 0.8859 (m-40) cc_final: 0.8457 (m-40)
REVERT: B  324 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8233 (mp0)
REVERT: B  351 ASP cc_start: 0.8312 (t0) cc_final: 0.7647 (m-30)
  outliers start: 21
  outliers final: 17
  residues processed: 130
  average time/residue: 0.2055
  time to fit residues: 37.3914
Evaluate side-chains
  130 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
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 E residue   30 THR
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue   96 THR
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  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:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 86 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9980
   chunk 17 optimal weight:   40.0000
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 HIS
B  65 HIS
** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.086239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.065902 restraints weight = 29928.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.068427 restraints weight = 16452.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.070130 restraints weight = 11619.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3530

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= 0.122
  Angle     :  0.629  13.645  11893  Z= 0.304
  Chirality :  0.046   0.203   1360
  Planarity :  0.004   0.034   1536
  Dihedral  :  3.855  19.692   1247
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 29.77 %
    Favored  : 67.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.78 (0.24), residues: 1150
  helix:  1.72 (0.36), residues: 216
  sheet: -1.26 (0.28), residues: 322
  loop : -0.87 (0.24), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 402 
 HIS   0.012   0.001   HIS C 176 
 PHE   0.017   0.001   PHE B 237 
 TYR   0.011   0.001   TYR B 173 
 ARG   0.008   0.000   ARG B 301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02895 (  261)
  hydrogen bonds       : angle       4.71425 (  729)
  covalent geometry    : bond        0.00286 ( 8717)
  covalent geometry    : angle       0.62881 (11893)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3112.36 seconds
wall clock time: 54 minutes 33.96 seconds (3273.96 seconds total)