Starting phenix.real_space_refine
on Fri Jul 25 14:55:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lun_63399/07_2025/9lun_63399.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lun_63399/07_2025/9lun_63399.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lun_63399/07_2025/9lun_63399.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lun_63399/07_2025/9lun_63399.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lun_63399/07_2025/9lun_63399.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lun_63399/07_2025/9lun_63399.cif"
  }
  resolution = 2.8
  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=   0.008
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      37      5.16       5
     C    4919      2.51       5
     N    1340      2.21       5
     O    1448      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 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: 7744
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 438, 3403
          Classifications: {'peptide': 438}
          Link IDs: {'PTRANS': 16, 'TRANS': 421}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2647
          Classifications: {'peptide': 334}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 315}
    Chain: "C"
      Number of atoms: 892
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 892
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 3, 'TRANS': 105}
    Chain: "D"
      Number of atoms: 777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 777
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'GA3': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.42, per 1000 atoms: 0.83
  Number of scatterers: 7744
  At special positions: 0
  Unit cell: (73.7649, 96.1179, 116.236, 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      37     16.00
     O    1448      8.00
     N    1340      7.00
     C    4919      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: 2.61
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1830

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 3 sheets defined
      59.3% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 58 through 76
    Processing helix  chain 'A' and resid 76 through 87
      removed outlier: 4.005A  pdb=" N   GLY A  80 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 108
    Processing helix  chain 'A' and resid 215 through 234
      removed outlier: 3.737A  pdb=" N   VAL A 219 " --> pdb=" O   GLN A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 254
      removed outlier: 3.909A  pdb=" N   ALA A 242 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL A 252 " --> pdb=" O   GLY A 248 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   SER A 253 " --> pdb=" O   CYS A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 277
      removed outlier: 4.217A  pdb=" N   LYS A 260 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR A 274 " --> pdb=" O   ALA A 270 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG A 275 " --> pdb=" O   ARG A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 295
    Processing helix  chain 'A' and resid 300 through 317
      removed outlier: 3.724A  pdb=" N   ALA A 312 " --> pdb=" O   THR A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 345
      removed outlier: 3.758A  pdb=" N   LEU A 339 " --> pdb=" O   GLN A 335 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLN A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
      removed outlier: 3.765A  pdb=" N   HIS A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLU A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA A 382 " --> pdb=" O   GLN A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 400
    Processing helix  chain 'A' and resid 401 through 406
      removed outlier: 3.619A  pdb=" N   MET A 404 " --> pdb=" O   ASP A 401 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU A 405 " --> pdb=" O   ALA A 402 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLU A 406 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 401 through 406'
    Processing helix  chain 'A' and resid 422 through 427
      removed outlier: 3.624A  pdb=" N   LEU A 427 " --> pdb=" O   HIS A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 444
      removed outlier: 3.564A  pdb=" N   LYS A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLN A 442 " --> pdb=" O   GLY A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 480
    Processing helix  chain 'A' and resid 486 through 505
    Processing helix  chain 'A' and resid 507 through 511
    Processing helix  chain 'A' and resid 517 through 529
    Processing helix  chain 'A' and resid 536 through 550
      removed outlier: 3.661A  pdb=" N   SER A 548 " --> pdb=" O   SER A 544 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   PHE A 550 " --> pdb=" O   LEU A 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 35
    Processing helix  chain 'B' and resid 42 through 50
    Processing helix  chain 'B' and resid 126 through 139
      removed outlier: 3.553A  pdb=" N   LEU B 130 " --> pdb=" O   ILE B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 170
      removed outlier: 3.592A  pdb=" N   TRP B 163 " --> pdb=" O   TYR B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 5.772A  pdb=" N   TRP B 174 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LYS B 176 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 207
    Processing helix  chain 'B' and resid 227 through 233
    Processing helix  chain 'B' and resid 240 through 252
    Processing helix  chain 'B' and resid 291 through 305
    Processing helix  chain 'B' and resid 320 through 324
      removed outlier: 3.520A  pdb=" N   LEU B 323 " --> pdb=" O   GLY B 320 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LEU B 324 " --> pdb=" O   PHE B 321 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 320 through 324'
    Processing helix  chain 'B' and resid 327 through 342
      removed outlier: 3.662A  pdb=" N   HIS B 331 " --> pdb=" O   ASN B 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 36 through 44
    Processing helix  chain 'C' and resid 49 through 56
    Processing helix  chain 'C' and resid 59 through 68
    Processing helix  chain 'C' and resid 68 through 79
      removed outlier: 4.340A  pdb=" N   TRP C  72 " --> pdb=" O   ASP C  68 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   HIS C  79 " --> pdb=" O   ILE C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 97
      removed outlier: 3.822A  pdb=" N   SER C  92 " --> pdb=" O   ASN C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 107
    Processing helix  chain 'C' and resid 107 through 113
    Processing helix  chain 'C' and resid 121 through 139
    Processing helix  chain 'D' and resid 51 through 65
      removed outlier: 4.135A  pdb=" N   ARG D  62 " --> pdb=" O   GLU D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 89 through 105
      removed outlier: 4.422A  pdb=" N   ASP D  93 " --> pdb=" O   SER D  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 120
      removed outlier: 3.544A  pdb=" N   LEU D 114 " --> pdb=" O   PHE D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 137
      removed outlier: 3.665A  pdb=" N   VAL D 132 " --> pdb=" O   THR D 128 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 148
      removed outlier: 3.960A  pdb=" N   PHE D 148 " --> pdb=" O   ILE D 144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 166
    Processing helix  chain 'D' and resid 166 through 171
      removed outlier: 3.673A  pdb=" N   PHE D 170 " --> pdb=" O   ASN D 166 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211
      removed outlier: 6.521A  pdb=" N   LEU B  76 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   LEU B  77 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL B 141 " --> pdb=" O   PRO B 107 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   VAL B 108 " --> pdb=" O   PHE B 186 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   ALA B 188 " --> pdb=" O   VAL B 108 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   LEU B 110 " --> pdb=" O   ALA B 188 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   ASP B 190 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   PHE B 112 " --> pdb=" O   ASP B 190 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   ILE B 185 " --> pdb=" O   GLY B 213 " (cutoff:3.500A)
      removed outlier: 8.667A  pdb=" N   ILE B 215 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   LEU B 187 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 8.245A  pdb=" N   LEU B 217 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   GLY B 189 " --> pdb=" O   LEU B 217 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   SER B 281 " --> pdb=" O   LYS B 310 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   MET B 312 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   VAL B 283 " --> pdb=" O   MET B 312 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   LEU B 314 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL B 285 " --> pdb=" O   LEU B 314 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 390
      removed outlier: 7.092A  pdb=" N   ARG A 322 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   ALA A 416 " --> pdb=" O   ARG A 322 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   HIS A 324 " --> pdb=" O   ALA A 416 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ASN A 418 " --> pdb=" O   HIS A 324 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ILE A 326 " --> pdb=" O   ASN A 418 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   VAL A 420 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ILE A 447 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR A 576 " --> pdb=" O   GLU A 452 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ALA A 579 " --> pdb=" O   ALA A 533 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390
      removed outlier: 7.092A  pdb=" N   ARG A 322 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   ALA A 416 " --> pdb=" O   ARG A 322 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   HIS A 324 " --> pdb=" O   ALA A 416 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   ASN A 418 " --> pdb=" O   HIS A 324 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ILE A 326 " --> pdb=" O   ASN A 418 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   VAL A 420 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ILE A 447 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR A 576 " --> pdb=" O   GLU A 452 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   TRP A 569 " --> pdb=" O   PRO A 573 " (cutoff:3.500A)

    432 hydrogen bonds defined for protein.
    1272 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: 2.08

  Time building geometry restraints manager: 2.37 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1386
        1.32 -     1.45: 2022
        1.45 -     1.57: 4447
        1.57 -     1.69: 1
        1.69 -     1.82: 57
  Bond restraints: 7913
  Sorted by residual:
  bond pdb=" C10 GA3 B 401 "
       pdb=" C9  GA3 B 401 "
    ideal  model  delta    sigma   weight residual
    1.506  1.560 -0.054 2.00e-02 2.50e+03 7.29e+00
  bond pdb=" CB  PRO D 141 "
       pdb=" CG  PRO D 141 "
    ideal  model  delta    sigma   weight residual
    1.492  1.601 -0.109 5.00e-02 4.00e+02 4.72e+00
  bond pdb=" C7  GA3 B 401 "
       pdb=" O72 GA3 B 401 "
    ideal  model  delta    sigma   weight residual
    1.248  1.216  0.032 2.00e-02 2.50e+03 2.48e+00
  bond pdb=" C7  GA3 B 401 "
       pdb=" O71 GA3 B 401 "
    ideal  model  delta    sigma   weight residual
    1.247  1.217  0.030 2.00e-02 2.50e+03 2.26e+00
  bond pdb=" CB  PRO C 110 "
       pdb=" CG  PRO C 110 "
    ideal  model  delta    sigma   weight residual
    1.492  1.566 -0.074 5.00e-02 4.00e+02 2.20e+00
  ... (remaining 7908 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 10541
        1.94 -     3.88: 151
        3.88 -     5.82: 25
        5.82 -     7.76: 11
        7.76 -     9.70: 3
  Bond angle restraints: 10731
  Sorted by residual:
  angle pdb=" CA  PRO C 110 "
        pdb=" N   PRO C 110 "
        pdb=" CD  PRO C 110 "
      ideal   model   delta    sigma   weight residual
     112.00  105.15    6.85 1.40e+00 5.10e-01 2.39e+01
  angle pdb=" CA  PRO D 141 "
        pdb=" N   PRO D 141 "
        pdb=" CD  PRO D 141 "
      ideal   model   delta    sigma   weight residual
     112.00  106.14    5.86 1.40e+00 5.10e-01 1.75e+01
  angle pdb=" CA  GLU C  73 "
        pdb=" CB  GLU C  73 "
        pdb=" CG  GLU C  73 "
      ideal   model   delta    sigma   weight residual
     114.10  120.75   -6.65 2.00e+00 2.50e-01 1.11e+01
  angle pdb=" CB  MET D 135 "
        pdb=" CG  MET D 135 "
        pdb=" SD  MET D 135 "
      ideal   model   delta    sigma   weight residual
     112.70  122.40   -9.70 3.00e+00 1.11e-01 1.05e+01
  angle pdb=" CA  LYS D  61 "
        pdb=" CB  LYS D  61 "
        pdb=" CG  LYS D  61 "
      ideal   model   delta    sigma   weight residual
     114.10  120.51   -6.41 2.00e+00 2.50e-01 1.03e+01
  ... (remaining 10726 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4098
       17.92 -    35.84: 508
       35.84 -    53.76: 153
       53.76 -    71.68: 30
       71.68 -    89.60: 15
  Dihedral angle restraints: 4804
    sinusoidal: 1976
      harmonic: 2828
  Sorted by residual:
  dihedral pdb=" CA  ARG A 271 "
           pdb=" C   ARG A 271 "
           pdb=" N   ARG A 272 "
           pdb=" CA  ARG A 272 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.33   18.67     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  GLN A  77 "
           pdb=" C   GLN A  77 "
           pdb=" N   GLU A  78 "
           pdb=" CA  GLU A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.62  -18.38     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CG  ARG B  73 "
           pdb=" CD  ARG B  73 "
           pdb=" NE  ARG B  73 "
           pdb=" CZ  ARG B  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -40.02  -49.98     2      1.50e+01 4.44e-03 1.25e+01
  ... (remaining 4801 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 1107
       0.079 -    0.157: 85
       0.157 -    0.236: 1
       0.236 -    0.315: 0
       0.315 -    0.394: 2
  Chirality restraints: 1195
  Sorted by residual:
  chirality pdb=" C5  GA3 B 401 "
            pdb=" C10 GA3 B 401 "
            pdb=" C4  GA3 B 401 "
            pdb=" C6  GA3 B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.80   -3.19    0.39 2.00e-01 2.50e+01 3.87e+00
  chirality pdb=" C9  GA3 B 401 "
            pdb=" C10 GA3 B 401 "
            pdb=" C11 GA3 B 401 "
            pdb=" C8  GA3 B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.24    2.57   -0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" C4  GA3 B 401 "
            pdb=" C19 GA3 B 401 "
            pdb=" C3  GA3 B 401 "
            pdb=" C5  GA3 B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      3.16    2.92    0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 1192 not shown)

  Planarity restraints: 1379
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C 109 "    0.076 5.00e-02 4.00e+02   1.11e-01 1.97e+01
        pdb=" N   PRO C 110 "   -0.192 5.00e-02 4.00e+02
        pdb=" CA  PRO C 110 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO C 110 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 140 "   -0.063 5.00e-02 4.00e+02   9.18e-02 1.35e+01
        pdb=" N   PRO D 141 "    0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO D 141 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO D 141 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS B 198 "   -0.009 2.00e-02 2.50e+03   1.85e-02 3.41e+00
        pdb=" C   HIS B 198 "    0.032 2.00e-02 2.50e+03
        pdb=" O   HIS B 198 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ASN B 199 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1376 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 141
        2.68 -     3.24: 7370
        3.24 -     3.79: 11927
        3.79 -     4.35: 16517
        4.35 -     4.90: 26946
  Nonbonded interactions: 62901
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 470 "
            pdb=" OG  SER A 474 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" O   PHE A 304 "
            pdb=" OG1 THR A 308 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   LEU A 463 "
            pdb=" OG1 THR A 467 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   HIS B 113 "
            pdb=" OH  TYR B 147 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   GLY A 508 "
            pdb=" NH2 ARG A 514 "
     model   vdw
     2.250 3.120
  ... (remaining 62896 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 individual isotropic
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:             4.070
  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:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.620
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
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   0.109   7913  Z= 0.149
  Angle     :  0.623   9.700  10731  Z= 0.323
  Chirality :  0.043   0.394   1195
  Planarity :  0.006   0.111   1379
  Dihedral  : 18.037  89.597   2974
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 25.65 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -1.02 (0.26), residues: 960
  helix: -0.53 (0.22), residues: 516
  sheet:  0.03 (0.50), residues: 106
  loop : -0.90 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP C  62 
 HIS   0.004   0.001   HIS A 424 
 PHE   0.030   0.001   PHE D 148 
 TYR   0.008   0.001   TYR B 127 
 ARG   0.009   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23503 (  414)
  hydrogen bonds       : angle       7.46999 ( 1272)
  covalent geometry    : bond        0.00364 ( 7913)
  covalent geometry    : angle       0.62302 (10731)

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6767 (mm-30)
REVERT: C   54 MET cc_start: 0.6320 (tpt) cc_final: 0.5778 (tpt)
REVERT: C   63 HIS cc_start: 0.6137 (t70) cc_final: 0.5924 (t70)
  outliers start: 24
  outliers final: 22
  residues processed: 109
  average time/residue: 1.0324
  time to fit residues: 120.5405
Evaluate side-chains
  102 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  396 SER
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  544 SER
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  171 SER
Chi-restraints excluded: chain B residue  218 ASN
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue  112 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0050
   chunk 38 optimal weight:    4.9990
   chunk 74 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    0.2980
   chunk 55 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.7996

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

Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 GLN
A 378 GLN
A 395 ASN
A 418 ASN
A 487 GLN
A 534 HIS
A 551 ASN
B 214 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.184342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.149498 restraints weight = 8079.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3767 rms_B_bonded: 1.62
r_work: 0.3589 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3472 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7913  Z= 0.149
  Angle     :  0.594   9.471  10731  Z= 0.309
  Chirality :  0.041   0.161   1195
  Planarity :  0.005   0.070   1379
  Dihedral  :  6.750  45.417   1161
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 22.92 %
    Favored  : 73.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.36 (0.27), residues: 960
  helix:  0.18 (0.22), residues: 529
  sheet:  0.20 (0.50), residues: 106
  loop : -0.89 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  21 
 HIS   0.005   0.001   HIS A 370 
 PHE   0.013   0.001   PHE D 148 
 TYR   0.018   0.002   TYR A 495 
 ARG   0.006   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05937 (  414)
  hydrogen bonds       : angle       5.15954 ( 1272)
  covalent geometry    : bond        0.00319 ( 7913)
  covalent geometry    : angle       0.59434 (10731)

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 101
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7624 (mp0)
REVERT: A  406 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7122 (mm-30)
REVERT: C   54 MET cc_start: 0.6480 (tpt) cc_final: 0.6192 (tpt)
  outliers start: 32
  outliers final: 17
  residues processed: 124
  average time/residue: 1.0836
  time to fit residues: 143.3000
Evaluate side-chains
  109 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 GLU
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  455 SER
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain D residue  140 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 68 optimal weight:    0.0020
   chunk 0 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 378 GLN
B 332 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.186194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.150689 restraints weight = 8263.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 1.65
r_work: 0.3608 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3493 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7913  Z= 0.122
  Angle     :  0.535   8.002  10731  Z= 0.278
  Chirality :  0.040   0.168   1195
  Planarity :  0.004   0.052   1379
  Dihedral  :  5.650  42.104   1143
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 22.09 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.06 (0.27), residues: 960
  helix:  0.57 (0.22), residues: 539
  sheet:  0.35 (0.50), residues: 108
  loop : -0.85 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A 424 
 PHE   0.010   0.001   PHE B 340 
 TYR   0.016   0.001   TYR A 495 
 ARG   0.008   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04830 (  414)
  hydrogen bonds       : angle       4.81138 ( 1272)
  covalent geometry    : bond        0.00264 ( 7913)
  covalent geometry    : angle       0.53492 (10731)

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 98
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  271 ARG cc_start: 0.7473 (ptm160) cc_final: 0.6713 (ptp-170)
  outliers start: 30
  outliers final: 15
  residues processed: 120
  average time/residue: 1.1431
  time to fit residues: 145.8662
Evaluate side-chains
  104 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  455 SER
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain D residue  140 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 47 optimal weight:    0.3980
   chunk 43 optimal weight:    0.0570
   chunk 6 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.187218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.152942 restraints weight = 8122.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 1.50
r_work: 0.3622 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7913  Z= 0.115
  Angle     :  0.513   6.417  10731  Z= 0.267
  Chirality :  0.039   0.149   1195
  Planarity :  0.004   0.046   1379
  Dihedral  :  5.028  42.054   1137
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 23.75 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.26 (0.27), residues: 960
  helix:  0.80 (0.22), residues: 541
  sheet:  0.35 (0.49), residues: 108
  loop : -0.89 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A 424 
 PHE   0.011   0.001   PHE B 340 
 TYR   0.013   0.001   TYR A 495 
 ARG   0.005   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04320 (  414)
  hydrogen bonds       : angle       4.61483 ( 1272)
  covalent geometry    : bond        0.00252 ( 7913)
  covalent geometry    : angle       0.51282 (10731)

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 ARG cc_start: 0.7465 (ptm160) cc_final: 0.6852 (ptp-170)
REVERT: A  292 GLN cc_start: 0.6248 (mp-120) cc_final: 0.6010 (mt0)
REVERT: A  491 MET cc_start: 0.8027 (mmm) cc_final: 0.7725 (mmp)
  outliers start: 24
  outliers final: 15
  residues processed: 116
  average time/residue: 1.0561
  time to fit residues: 130.8800
Evaluate side-chains
  106 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  455 SER
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  312 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0020
   chunk 32 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.9792

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

Flipped N/Q/H residues before XYZ refinement:
A 335 GLN
B 332 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.185198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.148533 restraints weight = 8087.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 1.78
r_work: 0.3618 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3497 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7913  Z= 0.140
  Angle     :  0.550   6.673  10731  Z= 0.283
  Chirality :  0.040   0.138   1195
  Planarity :  0.004   0.040   1379
  Dihedral  :  5.022  41.236   1136
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 22.57 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.19 (0.27), residues: 960
  helix:  0.75 (0.22), residues: 541
  sheet:  0.39 (0.49), residues: 108
  loop : -0.96 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  21 
 HIS   0.003   0.001   HIS A 424 
 PHE   0.013   0.001   PHE B 340 
 TYR   0.012   0.002   TYR A 473 
 ARG   0.009   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04670 (  414)
  hydrogen bonds       : angle       4.64730 ( 1272)
  covalent geometry    : bond        0.00323 ( 7913)
  covalent geometry    : angle       0.54990 (10731)

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 96
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LEU cc_start: 0.7694 (mp) cc_final: 0.7192 (mp)
REVERT: A  271 ARG cc_start: 0.7507 (ptm160) cc_final: 0.6878 (ptp-170)
REVERT: A  303 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8125 (mtmm)
REVERT: A  491 MET cc_start: 0.8024 (mmm) cc_final: 0.7737 (mmp)
  outliers start: 30
  outliers final: 16
  residues processed: 119
  average time/residue: 1.1595
  time to fit residues: 146.5866
Evaluate side-chains
  104 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  455 SER
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain D residue  140 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.186644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.150683 restraints weight = 8094.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.08
r_work: 0.3630 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7913  Z= 0.117
  Angle     :  0.532   7.381  10731  Z= 0.274
  Chirality :  0.039   0.130   1195
  Planarity :  0.004   0.042   1379
  Dihedral  :  4.637  18.736   1134
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 23.04 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.36 (0.27), residues: 960
  helix:  0.90 (0.22), residues: 542
  sheet:  0.47 (0.49), residues: 108
  loop : -0.91 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A 424 
 PHE   0.011   0.001   PHE D 148 
 TYR   0.012   0.001   TYR A 495 
 ARG   0.009   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04180 (  414)
  hydrogen bonds       : angle       4.52649 ( 1272)
  covalent geometry    : bond        0.00264 ( 7913)
  covalent geometry    : angle       0.53167 (10731)

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 93
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 ARG cc_start: 0.7360 (ptm160) cc_final: 0.6876 (ptp-170)
REVERT: A  292 GLN cc_start: 0.6145 (OUTLIER) cc_final: 0.5924 (mt0)
REVERT: A  491 MET cc_start: 0.7958 (mmm) cc_final: 0.7659 (mmp)
REVERT: A  513 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8287 (mm-30)
REVERT: D  117 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8293 (m-40)
  outliers start: 30
  outliers final: 17
  residues processed: 114
  average time/residue: 1.3329
  time to fit residues: 161.3236
Evaluate side-chains
  111 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  292 GLN
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  455 SER
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  513 GLU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain D residue  117 ASN
Chi-restraints excluded: chain D residue  140 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 87 optimal weight:    8.9990
   chunk 85 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0970
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
B 214 ASN
B 332 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.185613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.150178 restraints weight = 8171.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 1.56
r_work: 0.3615 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3502 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7913  Z= 0.128
  Angle     :  0.544   7.361  10731  Z= 0.280
  Chirality :  0.040   0.129   1195
  Planarity :  0.004   0.038   1379
  Dihedral  :  4.650  18.270   1134
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 23.99 %
    Favored  : 72.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.34 (0.27), residues: 960
  helix:  0.88 (0.22), residues: 542
  sheet:  0.47 (0.49), residues: 108
  loop : -0.91 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  21 
 HIS   0.003   0.001   HIS A 424 
 PHE   0.012   0.001   PHE D 148 
 TYR   0.012   0.001   TYR A 495 
 ARG   0.010   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04309 (  414)
  hydrogen bonds       : angle       4.53380 ( 1272)
  covalent geometry    : bond        0.00296 ( 7913)
  covalent geometry    : angle       0.54357 (10731)

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 1.993 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LEU cc_start: 0.7640 (mp) cc_final: 0.7159 (mp)
REVERT: A  271 ARG cc_start: 0.7339 (ptm160) cc_final: 0.6890 (ptp-170)
REVERT: A  292 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.6055 (mt0)
REVERT: A  303 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8065 (mtmm)
REVERT: A  491 MET cc_start: 0.7992 (mmm) cc_final: 0.7708 (mmp)
REVERT: A  513 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8306 (mm-30)
REVERT: D   92 GLU cc_start: 0.7787 (pm20) cc_final: 0.7538 (mp0)
REVERT: D  117 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8272 (m-40)
  outliers start: 28
  outliers final: 20
  residues processed: 114
  average time/residue: 1.3821
  time to fit residues: 167.3759
Evaluate side-chains
  112 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  292 GLN
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  455 SER
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  513 GLU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain D residue  117 ASN
Chi-restraints excluded: chain D residue  140 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0870
   chunk 14 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0470
   chunk 3 optimal weight:    7.9990
   chunk 16 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0980
   chunk 73 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
B 332 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.188473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.152686 restraints weight = 8163.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3815 rms_B_bonded: 1.59
r_work: 0.3641 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3526 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7913  Z= 0.107
  Angle     :  0.525   8.500  10731  Z= 0.269
  Chirality :  0.039   0.127   1195
  Planarity :  0.004   0.040   1379
  Dihedral  :  4.442  17.528   1134
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 23.87 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.54 (0.27), residues: 960
  helix:  1.08 (0.22), residues: 541
  sheet:  0.52 (0.49), residues: 108
  loop : -0.89 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A 424 
 PHE   0.013   0.001   PHE D 148 
 TYR   0.012   0.001   TYR A 495 
 ARG   0.010   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03781 (  414)
  hydrogen bonds       : angle       4.39753 ( 1272)
  covalent geometry    : bond        0.00236 ( 7913)
  covalent geometry    : angle       0.52456 (10731)

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.6838 (mtm) cc_final: 0.6582 (mtt)
REVERT: A  211 LEU cc_start: 0.7549 (mp) cc_final: 0.7093 (mp)
REVERT: A  271 ARG cc_start: 0.7338 (ptm160) cc_final: 0.6973 (ptp-170)
REVERT: A  292 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.6094 (mt0)
REVERT: A  303 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8101 (mtmm)
REVERT: A  491 MET cc_start: 0.8007 (mmm) cc_final: 0.7723 (mmp)
REVERT: D   92 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7528 (mp0)
REVERT: D  117 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8268 (m-40)
  outliers start: 27
  outliers final: 16
  residues processed: 114
  average time/residue: 1.1222
  time to fit residues: 136.3972
Evaluate side-chains
  110 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  292 GLN
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  455 SER
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain D residue   92 GLU
Chi-restraints excluded: chain D residue  117 ASN
Chi-restraints excluded: chain D residue  140 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 89 optimal weight:    0.2980
   chunk 81 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
B 214 ASN
B 332 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.186701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.150586 restraints weight = 8260.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 1.61
r_work: 0.3622 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3509 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7913  Z= 0.125
  Angle     :  0.552   8.803  10731  Z= 0.282
  Chirality :  0.040   0.147   1195
  Planarity :  0.004   0.039   1379
  Dihedral  :  4.451  17.420   1133
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 23.75 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.52 (0.27), residues: 960
  helix:  1.06 (0.22), residues: 541
  sheet:  0.53 (0.49), residues: 108
  loop : -0.90 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A 424 
 PHE   0.012   0.001   PHE D 148 
 TYR   0.011   0.001   TYR A 495 
 ARG   0.010   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04096 (  414)
  hydrogen bonds       : angle       4.43145 ( 1272)
  covalent geometry    : bond        0.00291 ( 7913)
  covalent geometry    : angle       0.55167 (10731)

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 88
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LEU cc_start: 0.7626 (mp) cc_final: 0.7176 (mp)
REVERT: A  271 ARG cc_start: 0.7334 (ptm160) cc_final: 0.6950 (ptp-170)
REVERT: A  292 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.6016 (mt0)
REVERT: A  303 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8111 (mtmm)
REVERT: A  406 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7056 (mm-30)
REVERT: A  491 MET cc_start: 0.8007 (mmm) cc_final: 0.7737 (mmp)
REVERT: D   92 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7517 (mp0)
REVERT: D  117 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8260 (m-40)
  outliers start: 27
  outliers final: 17
  residues processed: 107
  average time/residue: 1.4938
  time to fit residues: 169.6956
Evaluate side-chains
  107 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  292 GLN
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  455 SER
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain D residue   92 GLU
Chi-restraints excluded: chain D residue  117 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0770
   chunk 63 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    1.1340

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
B 214 ASN
B 332 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.185354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.149816 restraints weight = 8133.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 1.72
r_work: 0.3593 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3477 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7913  Z= 0.151
  Angle     :  0.591   9.048  10731  Z= 0.301
  Chirality :  0.041   0.153   1195
  Planarity :  0.004   0.038   1379
  Dihedral  :  4.621  17.464   1133
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 23.99 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.39 (0.27), residues: 960
  helix:  0.94 (0.22), residues: 539
  sheet:  0.65 (0.49), residues: 106
  loop : -1.00 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  21 
 HIS   0.003   0.001   HIS A 424 
 PHE   0.014   0.002   PHE B 340 
 TYR   0.013   0.002   TYR A 473 
 ARG   0.009   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04591 (  414)
  hydrogen bonds       : angle       4.50953 ( 1272)
  covalent geometry    : bond        0.00358 ( 7913)
  covalent geometry    : angle       0.59150 (10731)

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.6904 (mtm) cc_final: 0.6667 (mtt)
REVERT: A  211 LEU cc_start: 0.7635 (mp) cc_final: 0.7180 (mp)
REVERT: A  271 ARG cc_start: 0.7449 (ptm160) cc_final: 0.7063 (ptp-170)
REVERT: A  292 GLN cc_start: 0.6229 (OUTLIER) cc_final: 0.5996 (mt0)
REVERT: A  303 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8134 (mtmm)
REVERT: A  491 MET cc_start: 0.8053 (mmm) cc_final: 0.7775 (mmp)
REVERT: C   54 MET cc_start: 0.6371 (tpt) cc_final: 0.6157 (tpt)
REVERT: D   92 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7545 (mp0)
REVERT: D  117 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.8257 (m-40)
  outliers start: 26
  outliers final: 17
  residues processed: 107
  average time/residue: 1.3869
  time to fit residues: 157.9714
Evaluate side-chains
  108 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain A residue  292 GLN
Chi-restraints excluded: chain A residue  303 LYS
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  455 SER
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain B residue   19 ASN
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain D residue   92 GLU
Chi-restraints excluded: chain D residue  117 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0980
   chunk 20 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 214 ASN
B 332 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.186834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.150948 restraints weight = 8114.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 1.64
r_work: 0.3627 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3510 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7913  Z= 0.120
  Angle     :  0.562   8.870  10731  Z= 0.287
  Chirality :  0.040   0.132   1195
  Planarity :  0.004   0.039   1379
  Dihedral  :  4.480  17.328   1133
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 24.58 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.50 (0.27), residues: 960
  helix:  1.04 (0.22), residues: 542
  sheet:  0.50 (0.49), residues: 108
  loop : -0.91 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.004   0.001   HIS A 424 
 PHE   0.013   0.001   PHE D 148 
 TYR   0.012   0.001   TYR A 495 
 ARG   0.010   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04107 (  414)
  hydrogen bonds       : angle       4.41112 ( 1272)
  covalent geometry    : bond        0.00276 ( 7913)
  covalent geometry    : angle       0.56194 (10731)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6839.24 seconds
wall clock time: 122 minutes 0.57 seconds (7320.57 seconds total)