Starting phenix.real_space_refine
on Fri Feb 14 10:40:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qtj_14142/02_2025/7qtj_14142.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qtj_14142/02_2025/7qtj_14142.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qtj_14142/02_2025/7qtj_14142.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qtj_14142/02_2025/7qtj_14142.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qtj_14142/02_2025/7qtj_14142.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qtj_14142/02_2025/7qtj_14142.cif"
  }
  resolution = 4.01
  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=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    6285      2.51       5
     N    1673      2.21       5
     O    1942      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9942
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 1729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1729
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 11, 'TRANS': 216}
    Chain: "C"
      Number of atoms: 1640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1640
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 10, 'TRANS': 203}
    Chain: "A"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1612
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "D"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1612
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "E"
      Number of atoms: 1645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1645
          Classifications: {'peptide': 215}
          Link IDs: {'PTRANS': 12, 'TRANS': 202}
    Chain: "F"
      Number of atoms: 1637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1637
          Classifications: {'peptide': 221}
          Link IDs: {'PTRANS': 11, 'TRANS': 209}
    Chain: "G"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 6.32, per 1000 atoms: 0.64
  Number of scatterers: 9942
  At special positions: 0
  Unit cell: (82.998, 161.846, 152.163, 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      42     16.00
     O    1942      8.00
     N    1673      7.00
     C    6285      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 152 " - pdb=" SG  CYS B 208 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 228 " - pdb=" SG  CYS C 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 134 " - pdb=" SG  CYS C 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 336 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 379 " - pdb=" SG  CYS D 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 391 " - pdb=" SG  CYS D 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 480 " - pdb=" SG  CYS D 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 135 " - pdb=" SG  CYS E 195 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 101 " - pdb=" SG  CYS F 106 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 150 " - pdb=" SG  CYS F 206 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG G   1 " - " ASN A 343 "
      " NAG H   1 " - " ASN A 331 "
  Time building additional restraints: 2.66
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2366

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 26 sheets defined
      9.8% alpha, 34.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.40
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.656A  pdb=" N   ASP B  31 " --> pdb=" O   ARG B  28 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   TYR B  32 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 28 through 32'
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 4.043A  pdb=" N   THR B  91 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 141
      No H-bonds generated for 'chain 'B' and resid 139 through 141'
    Processing helix  chain 'B' and resid 168 through 170
      No H-bonds generated for 'chain 'B' and resid 168 through 170'
    Processing helix  chain 'B' and resid 199 through 201
      No H-bonds generated for 'chain 'B' and resid 199 through 201'
    Processing helix  chain 'C' and resid 79 through 83
      removed outlier: 3.741A  pdb=" N   PHE C  83 " --> pdb=" O   PRO C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 127
      removed outlier: 3.529A  pdb=" N   SER C 127 " --> pdb=" O   GLU C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 187
      removed outlier: 4.083A  pdb=" N   GLU C 187 " --> pdb=" O   LYS C 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 183 through 187'
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 4.414A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 370
    Processing helix  chain 'A' and resid 403 through 410
      removed outlier: 3.838A  pdb=" N   VAL A 407 " --> pdb=" O   ARG A 403 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   ARG A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'D' and resid 365 through 371
      removed outlier: 3.897A  pdb=" N   TYR D 369 " --> pdb=" O   TYR D 365 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 383 through 387
      removed outlier: 3.677A  pdb=" N   LEU D 387 " --> pdb=" O   PRO D 384 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 410
      removed outlier: 4.196A  pdb=" N   ARG D 408 " --> pdb=" O   ASP D 405 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE D 410 " --> pdb=" O   VAL D 407 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 416 through 422
    Processing helix  chain 'E' and resid 80 through 84
      removed outlier: 3.900A  pdb=" N   PHE E  84 " --> pdb=" O   PRO E  81 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 128
    Processing helix  chain 'E' and resid 184 through 189
    Processing helix  chain 'F' and resid 28 through 31
    Processing helix  chain 'F' and resid 87 through 91
      removed outlier: 3.783A  pdb=" N   THR F  91 " --> pdb=" O   SER F  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 137 through 141
    Processing helix  chain 'F' and resid 166 through 168
      No H-bonds generated for 'chain 'F' and resid 166 through 168'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7
      removed outlier: 3.571A  pdb=" N   LEU B  18 " --> pdb=" O   MET B  83 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.666A  pdb=" N   LEU B  34 " --> pdb=" O   ILE B  51 " (cutoff:3.500A)
      removed outlier: 5.708A  pdb=" N   ARG B  38 " --> pdb=" O   TRP B  47 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   TRP B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLY B  50 " --> pdb=" O   GLY B  59 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLY B  59 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.550A  pdb=" N   LYS B  98 " --> pdb=" O   ASP B 113 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 132 through 136
      removed outlier: 3.567A  pdb=" N   PHE B 134 " --> pdb=" O   LEU B 153 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU B 153 " --> pdb=" O   PHE B 134 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   GLY B 151 " --> pdb=" O   LEU B 136 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ASP B 156 " --> pdb=" O   TYR B 188 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   TYR B 188 " --> pdb=" O   ASP B 156 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 143 through 144
      removed outlier: 3.526A  pdb=" N   ASP B 156 " --> pdb=" O   TYR B 188 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   TYR B 188 " --> pdb=" O   ASP B 156 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166
      removed outlier: 3.624A  pdb=" N   SER B 165 " --> pdb=" O   ASN B 209 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   CYS B 208 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 6
      removed outlier: 3.898A  pdb=" N   VAL C  19 " --> pdb=" O   ILE C  75 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.325A  pdb=" N   LEU C  11 " --> pdb=" O   ASP C 105 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   VAL C  33 " --> pdb=" O   TYR C  49 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   TYR C  49 " --> pdb=" O   VAL C  33 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   TRP C  35 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 114 through 118
      removed outlier: 3.844A  pdb=" N   VAL C 133 " --> pdb=" O   PHE C 118 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 153 through 155
      removed outlier: 4.171A  pdb=" N   TRP C 148 " --> pdb=" O   GLN C 155 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   TYR C 192 " --> pdb=" O   PHE C 209 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   CYS C 194 " --> pdb=" O   LYS C 207 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   LYS C 207 " --> pdb=" O   CYS C 194 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL C 196 " --> pdb=" O   VAL C 205 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL C 205 " --> pdb=" O   VAL C 196 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.913A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA A 435 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.524A  pdb=" N   TYR A 473 " --> pdb=" O   TYR A 489 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'D' and resid 356 through 358
      removed outlier: 3.776A  pdb=" N   VAL D 395 " --> pdb=" O   ILE D 358 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   TYR D 396 " --> pdb=" O   SER D 514 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   SER D 514 " --> pdb=" O   TYR D 396 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 452 through 454
    Processing sheet with id=AB7, first strand: chain 'D' and resid 473 through 474
      removed outlier: 3.793A  pdb=" N   TYR D 473 " --> pdb=" O   TYR D 489 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   TYR D 489 " --> pdb=" O   TYR D 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 6
    Processing sheet with id=AB9, first strand: chain 'E' and resid 46 through 49
      removed outlier: 6.282A  pdb=" N   TRP E  36 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 115 through 119
      removed outlier: 4.386A  pdb=" N   SER E 175 " --> pdb=" O   THR E 165 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   THR E 165 " --> pdb=" O   SER E 175 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 154 through 156
      removed outlier: 4.449A  pdb=" N   TRP E 149 " --> pdb=" O   GLN E 156 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 6
    Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12
      removed outlier: 4.182A  pdb=" N   GLY F  49 " --> pdb=" O   TRP F  36 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ARG F  38 " --> pdb=" O   TRP F  47 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   TRP F  47 " --> pdb=" O   ARG F  38 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 12
    Processing sheet with id=AC6, first strand: chain 'F' and resid 130 through 134
      removed outlier: 6.188A  pdb=" N   TYR F 186 " --> pdb=" O   ASP F 154 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'F' and resid 130 through 134
      removed outlier: 6.188A  pdb=" N   TYR F 186 " --> pdb=" O   ASP F 154 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 161 through 164

    334 hydrogen bonds defined for protein.
    822 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: 3.20

  Time building geometry restraints manager: 3.11 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2750
        1.33 -     1.45: 1966
        1.45 -     1.58: 5425
        1.58 -     1.70: 1
        1.70 -     1.82: 47
  Bond restraints: 10189
  Sorted by residual:
  bond pdb=" CG  PRO E 121 "
       pdb=" CD  PRO E 121 "
    ideal  model  delta    sigma   weight residual
    1.503  1.299  0.204 3.40e-02 8.65e+02 3.59e+01
  bond pdb=" CA  SER B  52 "
       pdb=" CB  SER B  52 "
    ideal  model  delta    sigma   weight residual
    1.531  1.464  0.066 1.48e-02 4.57e+03 2.00e+01
  bond pdb=" N   PRO E 121 "
       pdb=" CD  PRO E 121 "
    ideal  model  delta    sigma   weight residual
    1.473  1.519 -0.046 1.40e-02 5.10e+03 1.09e+01
  bond pdb=" CB  PRO E 121 "
       pdb=" CG  PRO E 121 "
    ideal  model  delta    sigma   weight residual
    1.492  1.645 -0.153 5.00e-02 4.00e+02 9.37e+00
  bond pdb=" CA  SER B  55 "
       pdb=" CB  SER B  55 "
    ideal  model  delta    sigma   weight residual
    1.532  1.488  0.044 1.48e-02 4.57e+03 8.97e+00
  ... (remaining 10184 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.92: 13784
        3.92 -     7.83: 66
        7.83 -    11.75: 3
       11.75 -    15.67: 3
       15.67 -    19.59: 1
  Bond angle restraints: 13857
  Sorted by residual:
  angle pdb=" CA  PRO E 121 "
        pdb=" N   PRO E 121 "
        pdb=" CD  PRO E 121 "
      ideal   model   delta    sigma   weight residual
     112.00   96.57   15.43 1.40e+00 5.10e-01 1.22e+02
  angle pdb=" CG  ARG A 346 "
        pdb=" CD  ARG A 346 "
        pdb=" NE  ARG A 346 "
      ideal   model   delta    sigma   weight residual
     112.00   92.41   19.59 2.20e+00 2.07e-01 7.93e+01
  angle pdb=" N   PRO E 121 "
        pdb=" CD  PRO E 121 "
        pdb=" CG  PRO E 121 "
      ideal   model   delta    sigma   weight residual
     103.20   90.73   12.47 1.50e+00 4.44e-01 6.91e+01
  angle pdb=" C   PHE A 377 "
        pdb=" CA  PHE A 377 "
        pdb=" CB  PHE A 377 "
      ideal   model   delta    sigma   weight residual
     111.85   99.84   12.01 1.47e+00 4.63e-01 6.68e+01
  angle pdb=" C   THR C 172 "
        pdb=" CA  THR C 172 "
        pdb=" CB  THR C 172 "
      ideal   model   delta    sigma   weight residual
     114.40  106.53    7.87 1.25e+00 6.40e-01 3.97e+01
  ... (remaining 13852 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.98: 5676
       21.98 -    43.95: 381
       43.95 -    65.93: 51
       65.93 -    87.90: 22
       87.90 -   109.88: 9
  Dihedral angle restraints: 6139
    sinusoidal: 2431
      harmonic: 3708
  Sorted by residual:
  dihedral pdb=" CB  CYS B 152 "
           pdb=" SG  CYS B 152 "
           pdb=" SG  CYS B 208 "
           pdb=" CB  CYS B 208 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.95  -66.95     1      1.00e+01 1.00e-02 5.84e+01
  dihedral pdb=" C   PHE A 377 "
           pdb=" N   PHE A 377 "
           pdb=" CA  PHE A 377 "
           pdb=" CB  PHE A 377 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.54  -15.06     0      2.50e+00 1.60e-01 3.63e+01
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -131.63   45.63     1      1.00e+01 1.00e-02 2.89e+01
  ... (remaining 6136 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1416
       0.091 -    0.181: 110
       0.181 -    0.272: 9
       0.272 -    0.362: 3
       0.362 -    0.453: 2
  Chirality restraints: 1540
  Sorted by residual:
  chirality pdb=" CA  PHE A 377 "
            pdb=" N   PHE A 377 "
            pdb=" C   PHE A 377 "
            pdb=" CB  PHE A 377 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.96   -0.45 2.00e-01 2.50e+01 5.13e+00
  chirality pdb=" CA  ARG A 346 "
            pdb=" N   ARG A 346 "
            pdb=" C   ARG A 346 "
            pdb=" CB  ARG A 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.37 2.00e-01 2.50e+01 3.39e+00
  chirality pdb=" CA  ARG B  72 "
            pdb=" N   ARG B  72 "
            pdb=" C   ARG B  72 "
            pdb=" CB  ARG B  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.66e+00
  ... (remaining 1537 not shown)

  Planarity restraints: 1782
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E 120 "   -0.100 5.00e-02 4.00e+02   1.37e-01 2.99e+01
        pdb=" N   PRO E 121 "    0.236 5.00e-02 4.00e+02
        pdb=" CA  PRO E 121 "   -0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO E 121 "   -0.072 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS B 101 "   -0.022 2.00e-02 2.50e+03   4.37e-02 1.91e+01
        pdb=" C   HIS B 101 "    0.076 2.00e-02 2.50e+03
        pdb=" O   HIS B 101 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   TYR B 102 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  51 "    0.021 2.00e-02 2.50e+03   4.13e-02 1.71e+01
        pdb=" C   ILE B  51 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   ILE B  51 "    0.027 2.00e-02 2.50e+03
        pdb=" N   SER B  52 "    0.024 2.00e-02 2.50e+03
  ... (remaining 1779 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 246
        2.70 -     3.25: 9271
        3.25 -     3.80: 14986
        3.80 -     4.35: 19152
        4.35 -     4.90: 31923
  Nonbonded interactions: 75578
  Sorted by model distance:
  nonbonded pdb=" CB  ARG A 346 "
            pdb=" NE  ARG A 346 "
     model   vdw
     2.144 2.816
  nonbonded pdb=" OE1 GLN C   6 "
            pdb=" OG1 THR C 102 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   PRO B 197 "
            pdb=" OG  SER B 200 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" NH1 ARG D 403 "
            pdb=" O   GLY D 504 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" OE2 GLU B   6 "
            pdb=" N   GLY B 118 "
     model   vdw
     2.315 3.120
  ... (remaining 75573 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.010
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.050
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
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   0.204  10189  Z= 0.318
  Angle     :  0.727  19.587  13857  Z= 0.422
  Chirality :  0.050   0.453   1540
  Planarity :  0.005   0.137   1780
  Dihedral  : 15.202 109.878   3719
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.21 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  0.54 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.34 %
  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:  0.17 (0.25), residues: 1268
  helix: -2.11 (0.56), residues: 62
  sheet:  1.33 (0.25), residues: 440
  loop : -0.43 (0.24), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 148 
 HIS   0.002   0.001   HIS C  92 
 PHE   0.029   0.001   PHE A 377 
 TYR   0.025   0.001   TYR B 102 
 ARG   0.005   0.000   ARG F  38 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  167 ASP cc_start: 0.8876 (m-30) cc_final: 0.8606 (m-30)
REVERT: A  375 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.6655 (p90)
REVERT: D  375 PHE cc_start: 0.5919 (m-10) cc_final: 0.5478 (m-80)
REVERT: F   10 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7425 (mm-30)
  outliers start: 14
  outliers final: 4
  residues processed: 131
  average time/residue: 0.2520
  time to fit residues: 45.2936
Evaluate side-chains
  85 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 1.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 95 optimal weight:    0.1980
   chunk 52 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 98 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0020
   chunk 73 optimal weight:    9.9990
   chunk 114 optimal weight:    7.9990
   overall best weight:    1.0192

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

Flipped N/Q/H residues before XYZ refinement:
B 167 ASN
C   6 GLN
C 138 ASN
** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 166 GLN
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  91 GLN
E 101 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.119990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.099915 restraints weight = 35208.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.099675 restraints weight = 32855.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.100283 restraints weight = 28653.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.0940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  10189  Z= 0.164
  Angle     :  0.596  14.381  13857  Z= 0.300
  Chirality :  0.045   0.400   1540
  Planarity :  0.004   0.049   1780
  Dihedral  :  8.126  77.934   1497
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.57 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  5.26 %
    Favored  : 94.46 %
  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:  0.18 (0.24), residues: 1268
  helix: -2.20 (0.55), residues: 60
  sheet:  1.29 (0.25), residues: 458
  loop : -0.42 (0.24), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  53 
 HIS   0.003   0.001   HIS B 101 
 PHE   0.017   0.001   PHE D 429 
 TYR   0.014   0.001   TYR B 102 
 ARG   0.004   0.000   ARG F  38 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 122
  time to evaluate  : 1.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.8521 (p0) cc_final: 0.8247 (p0)
REVERT: A  389 ASP cc_start: 0.9224 (p0) cc_final: 0.8570 (p0)
REVERT: A  392 PHE cc_start: 0.8022 (m-80) cc_final: 0.7740 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 125
  average time/residue: 0.2281
  time to fit residues: 40.0931
Evaluate side-chains
  83 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 33 optimal weight:    0.3980
   chunk 115 optimal weight:    5.9990
   chunk 107 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0980
   chunk 44 optimal weight:    4.9990
   chunk 67 optimal weight:    8.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 ASN
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 460 ASN
D 487 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.115177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.095629 restraints weight = 36116.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.096946 restraints weight = 37189.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.097302 restraints weight = 31010.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10189  Z= 0.293
  Angle     :  0.671  10.921  13857  Z= 0.345
  Chirality :  0.046   0.269   1540
  Planarity :  0.004   0.044   1780
  Dihedral  :  6.830  56.156   1497
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.68 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.54 %
    Favored  : 94.28 %
  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: -0.20 (0.24), residues: 1268
  helix: -2.11 (0.62), residues: 54
  sheet:  0.74 (0.24), residues: 473
  loop : -0.55 (0.24), residues: 741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  53 
 HIS   0.005   0.001   HIS E 199 
 PHE   0.023   0.002   PHE F  29 
 TYR   0.016   0.002   TYR F 155 
 ARG   0.012   0.001   ARG A 403 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.8588 (p0) cc_final: 0.8295 (p0)
REVERT: B   99 ASP cc_start: 0.8843 (t0) cc_final: 0.8446 (t0)
REVERT: C  194 CYS cc_start: -0.0052 (p) cc_final: -0.0705 (p)
REVERT: A  389 ASP cc_start: 0.9236 (p0) cc_final: 0.8680 (p0)
REVERT: A  392 PHE cc_start: 0.8165 (m-80) cc_final: 0.7844 (m-80)
REVERT: A  406 GLU cc_start: 0.8894 (mp0) cc_final: 0.8589 (mm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 115
  average time/residue: 0.2566
  time to fit residues: 40.3995
Evaluate side-chains
  79 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 93 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 111 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 76 optimal weight:    9.9990
   chunk 117 optimal weight:    0.0770
   chunk 3 optimal weight:    2.9990
   overall best weight:    2.2146

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

Flipped N/Q/H residues before XYZ refinement:
** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.116568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.098067 restraints weight = 35622.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.099031 restraints weight = 38377.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.099303 restraints weight = 31590.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10189  Z= 0.233
  Angle     :  0.631  10.516  13857  Z= 0.323
  Chirality :  0.046   0.304   1540
  Planarity :  0.004   0.037   1780
  Dihedral  :  6.310  59.850   1497
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.36 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.54 %
    Favored  : 96.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.24), residues: 1268
  helix: -2.29 (0.57), residues: 61
  sheet:  0.73 (0.24), residues: 476
  loop : -0.64 (0.24), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 436 
 HIS   0.003   0.001   HIS E 199 
 PHE   0.036   0.002   PHE C  71 
 TYR   0.017   0.002   TYR B 102 
 ARG   0.005   0.001   ARG D 493 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   99 ASP cc_start: 0.8734 (t0) cc_final: 0.8297 (t0)
REVERT: C   14 SER cc_start: 0.8780 (p) cc_final: 0.8443 (m)
REVERT: C  140 TYR cc_start: 0.6893 (t80) cc_final: 0.6531 (t80)
REVERT: C  145 LYS cc_start: 0.8493 (tppt) cc_final: 0.8233 (tppt)
REVERT: C  194 CYS cc_start: 0.0033 (p) cc_final: -0.0803 (p)
REVERT: A  389 ASP cc_start: 0.9236 (p0) cc_final: 0.8695 (p0)
REVERT: A  392 PHE cc_start: 0.8124 (m-80) cc_final: 0.7793 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 123
  average time/residue: 0.2492
  time to fit residues: 41.8407
Evaluate side-chains
  85 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 48 optimal weight:    0.0040
   chunk 13 optimal weight:    8.9990
   chunk 81 optimal weight:    9.9990
   chunk 65 optimal weight:    4.9990
   chunk 32 optimal weight:    8.9990
   chunk 92 optimal weight:    0.7980
   chunk 55 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0980
   chunk 62 optimal weight:    7.9990
   overall best weight:    1.3594

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

Flipped N/Q/H residues before XYZ refinement:
** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.116804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.097118 restraints weight = 35660.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.098328 restraints weight = 34422.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.098519 restraints weight = 32298.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10189  Z= 0.179
  Angle     :  0.607  11.272  13857  Z= 0.307
  Chirality :  0.045   0.288   1540
  Planarity :  0.004   0.036   1780
  Dihedral  :  5.964  58.776   1497
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.21 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.24), residues: 1268
  helix: -2.10 (0.62), residues: 55
  sheet:  0.71 (0.24), residues: 479
  loop : -0.54 (0.24), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 436 
 HIS   0.002   0.000   HIS B 101 
 PHE   0.026   0.001   PHE C  71 
 TYR   0.014   0.001   TYR B 102 
 ARG   0.002   0.000   ARG E 212 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 1.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.8617 (p0) cc_final: 0.8377 (p0)
REVERT: B   99 ASP cc_start: 0.8733 (t0) cc_final: 0.8361 (t0)
REVERT: C   14 SER cc_start: 0.8686 (p) cc_final: 0.8436 (m)
REVERT: C   70 GLU cc_start: 0.8574 (tt0) cc_final: 0.8088 (tm-30)
REVERT: C  140 TYR cc_start: 0.6880 (t80) cc_final: 0.6401 (t80)
REVERT: C  194 CYS cc_start: -0.0347 (p) cc_final: -0.0817 (p)
REVERT: A  389 ASP cc_start: 0.9272 (p0) cc_final: 0.8748 (p0)
REVERT: A  392 PHE cc_start: 0.8160 (m-80) cc_final: 0.7793 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.2613
  time to fit residues: 43.0004
Evaluate side-chains
  80 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    0.0970
   chunk 122 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 68 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0670
   chunk 25 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    2.6322

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

Flipped N/Q/H residues before XYZ refinement:
B 209 ASN
** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 HIS
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  91 GLN
F 100 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.114006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.094150 restraints weight = 35627.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.094828 restraints weight = 36479.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.095219 restraints weight = 35880.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10189  Z= 0.269
  Angle     :  0.662  10.910  13857  Z= 0.341
  Chirality :  0.046   0.291   1540
  Planarity :  0.004   0.047   1780
  Dihedral  :  6.014  59.245   1497
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.55 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.36 %
    Favored  : 96.55 %
  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: -0.46 (0.24), residues: 1268
  helix: -2.26 (0.63), residues: 55
  sheet:  0.51 (0.24), residues: 481
  loop : -0.69 (0.24), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 436 
 HIS   0.005   0.001   HIS E 199 
 PHE   0.028   0.002   PHE C  71 
 TYR   0.024   0.002   TYR E  33 
 ARG   0.010   0.001   ARG C  61 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 1.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   99 ASP cc_start: 0.8797 (t0) cc_final: 0.8393 (t0)
REVERT: C   14 SER cc_start: 0.8824 (p) cc_final: 0.8599 (m)
REVERT: C  145 LYS cc_start: 0.8709 (tppt) cc_final: 0.8345 (tppt)
REVERT: C  194 CYS cc_start: -0.0163 (p) cc_final: -0.0679 (p)
REVERT: A  389 ASP cc_start: 0.9242 (p0) cc_final: 0.8808 (p0)
REVERT: A  392 PHE cc_start: 0.8106 (m-80) cc_final: 0.7674 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2714
  time to fit residues: 40.6486
Evaluate side-chains
  79 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 61 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 112 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 109 optimal weight:    0.8980
   chunk 20 optimal weight:    8.9990
   chunk 116 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.116343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.096457 restraints weight = 36316.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.096618 restraints weight = 35666.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.096937 restraints weight = 38291.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10189  Z= 0.159
  Angle     :  0.608   8.809  13857  Z= 0.307
  Chirality :  0.044   0.221   1540
  Planarity :  0.004   0.038   1780
  Dihedral  :  5.670  57.788   1497
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.81 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.72 %
    Favored  : 98.19 %
  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: -0.37 (0.24), residues: 1268
  helix: -2.36 (0.57), residues: 61
  sheet:  0.59 (0.24), residues: 475
  loop : -0.60 (0.24), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B 101 
 PHE   0.024   0.001   PHE D 392 
 TYR   0.017   0.001   TYR F 155 
 ARG   0.006   0.000   ARG B 222 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   99 ASP cc_start: 0.8746 (t0) cc_final: 0.8411 (t0)
REVERT: C   14 SER cc_start: 0.8773 (p) cc_final: 0.8517 (m)
REVERT: C   70 GLU cc_start: 0.8572 (tt0) cc_final: 0.8094 (tm-30)
REVERT: C  145 LYS cc_start: 0.8731 (tppt) cc_final: 0.8457 (tppt)
REVERT: C  194 CYS cc_start: -0.0383 (p) cc_final: -0.0886 (p)
REVERT: A  389 ASP cc_start: 0.9250 (p0) cc_final: 0.8807 (p0)
REVERT: A  392 PHE cc_start: 0.8108 (m-80) cc_final: 0.7661 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 114
  average time/residue: 0.2551
  time to fit residues: 40.0536
Evaluate side-chains
  82 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 76 optimal weight:    0.2980
   chunk 93 optimal weight:    6.9990
   chunk 108 optimal weight:    0.0010
   chunk 7 optimal weight:    0.7980
   chunk 125 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 166 GLN
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.117470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.097991 restraints weight = 35720.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.098824 restraints weight = 34498.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.099231 restraints weight = 30187.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10189  Z= 0.144
  Angle     :  0.595   9.255  13857  Z= 0.297
  Chirality :  0.044   0.237   1540
  Planarity :  0.004   0.035   1780
  Dihedral  :  5.393  57.906   1497
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.81 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  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: -0.28 (0.24), residues: 1268
  helix: -2.37 (0.56), residues: 61
  sheet:  0.75 (0.25), residues: 460
  loop : -0.59 (0.24), residues: 747

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 149 
 HIS   0.002   0.000   HIS B 212 
 PHE   0.019   0.001   PHE C  71 
 TYR   0.014   0.001   TYR E  33 
 ARG   0.006   0.000   ARG B 222 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.8695 (p0) cc_final: 0.8470 (p0)
REVERT: B   99 ASP cc_start: 0.8691 (t0) cc_final: 0.8298 (t0)
REVERT: C   14 SER cc_start: 0.8642 (p) cc_final: 0.8354 (m)
REVERT: C   70 GLU cc_start: 0.8585 (tt0) cc_final: 0.8128 (tm-30)
REVERT: C  145 LYS cc_start: 0.8698 (tppt) cc_final: 0.8407 (tppt)
REVERT: C  194 CYS cc_start: -0.0372 (p) cc_final: -0.0923 (p)
REVERT: A  389 ASP cc_start: 0.9278 (p0) cc_final: 0.8832 (p0)
REVERT: D  454 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7956 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.2669
  time to fit residues: 42.8486
Evaluate side-chains
  87 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 123 optimal weight:    0.9980
   chunk 14 optimal weight:   20.0000
   chunk 80 optimal weight:   20.0000
   chunk 119 optimal weight:    5.9990
   chunk 121 optimal weight:    5.9990
   chunk 118 optimal weight:    5.9990
   chunk 39 optimal weight:   20.0000
   chunk 63 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0570
   chunk 15 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0980
   overall best weight:    0.8100

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

Flipped N/Q/H residues before XYZ refinement:
** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.117324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.097540 restraints weight = 35897.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.098388 restraints weight = 34261.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.098721 restraints weight = 31147.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  10189  Z= 0.157
  Angle     :  0.590   7.214  13857  Z= 0.297
  Chirality :  0.044   0.189   1540
  Planarity :  0.004   0.034   1780
  Dihedral  :  5.223  55.742   1497
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.89 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  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: -0.32 (0.24), residues: 1268
  helix: -2.34 (0.56), residues: 61
  sheet:  0.76 (0.25), residues: 458
  loop : -0.64 (0.23), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.003   0.000   HIS B  35 
 PHE   0.020   0.001   PHE D 392 
 TYR   0.017   0.001   TYR C 140 
 ARG   0.005   0.000   ARG A 509 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.8631 (p0) cc_final: 0.8378 (p0)
REVERT: B   99 ASP cc_start: 0.8789 (t0) cc_final: 0.8432 (t0)
REVERT: C   70 GLU cc_start: 0.8465 (tt0) cc_final: 0.8025 (tm-30)
REVERT: C  107 GLU cc_start: 0.7564 (tp30) cc_final: 0.7290 (tp30)
REVERT: C  145 LYS cc_start: 0.8785 (tppt) cc_final: 0.8463 (tppt)
REVERT: A  389 ASP cc_start: 0.9286 (p0) cc_final: 0.8827 (p0)
REVERT: D  454 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7948 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.2567
  time to fit residues: 41.5860
Evaluate side-chains
  82 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 118 optimal weight:    9.9990
   chunk 69 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0870
   chunk 109 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0170
   chunk 82 optimal weight:    3.9990
   chunk 104 optimal weight:   10.0000
   overall best weight:    2.1600

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

Flipped N/Q/H residues before XYZ refinement:
** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.115262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.095242 restraints weight = 35988.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.095882 restraints weight = 34182.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.096179 restraints weight = 33920.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10189  Z= 0.228
  Angle     :  0.620   6.559  13857  Z= 0.315
  Chirality :  0.044   0.207   1540
  Planarity :  0.004   0.039   1780
  Dihedral  :  5.388  55.954   1497
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.84 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  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: -0.42 (0.24), residues: 1268
  helix: -2.35 (0.57), residues: 61
  sheet:  0.66 (0.25), residues: 461
  loop : -0.71 (0.24), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 353 
 HIS   0.003   0.001   HIS E 199 
 PHE   0.025   0.002   PHE D 429 
 TYR   0.016   0.001   TYR B  94 
 ARG   0.005   0.000   ARG A 509 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 1.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.8732 (p0) cc_final: 0.8498 (p0)
REVERT: B   99 ASP cc_start: 0.8773 (t0) cc_final: 0.8407 (t0)
REVERT: C   70 GLU cc_start: 0.8446 (tt0) cc_final: 0.8027 (tm-30)
REVERT: C  107 GLU cc_start: 0.7649 (tp30) cc_final: 0.7392 (tp30)
REVERT: C  194 CYS cc_start: 0.0768 (p) cc_final: -0.0188 (p)
REVERT: A  389 ASP cc_start: 0.9228 (p0) cc_final: 0.8757 (p0)
REVERT: A  392 PHE cc_start: 0.8185 (m-80) cc_final: 0.7755 (m-80)
REVERT: D  375 PHE cc_start: 0.4820 (m-80) cc_final: 0.4566 (m-80)
REVERT: D  454 ARG cc_start: 0.8223 (tpp80) cc_final: 0.7988 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.2695
  time to fit residues: 40.6977
Evaluate side-chains
  82 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 115 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0270
   chunk 56 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0870
   chunk 114 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 35 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.117452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.097720 restraints weight = 35791.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.098521 restraints weight = 34354.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.098993 restraints weight = 30024.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10189  Z= 0.152
  Angle     :  0.599   6.489  13857  Z= 0.300
  Chirality :  0.044   0.173   1540
  Planarity :  0.004   0.035   1780
  Dihedral  :  5.133  52.305   1497
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.57 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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: -0.35 (0.24), residues: 1268
  helix: -2.41 (0.56), residues: 61
  sheet:  0.77 (0.25), residues: 461
  loop : -0.69 (0.24), residues: 746

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.002   0.000   HIS B  35 
 PHE   0.018   0.001   PHE C  71 
 TYR   0.020   0.001   TYR F 155 
 ARG   0.004   0.000   ARG B 222 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2824.17 seconds
wall clock time: 52 minutes 10.18 seconds (3130.18 seconds total)