Starting phenix.real_space_refine
on Sun Apr  5 03:52:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j5n_61147/04_2026/9j5n_61147.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j5n_61147/04_2026/9j5n_61147.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j5n_61147/04_2026/9j5n_61147.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j5n_61147/04_2026/9j5n_61147.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j5n_61147/04_2026/9j5n_61147.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j5n_61147/04_2026/9j5n_61147.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.082
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: 5
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     S      33      5.16       5
     C    5017      2.51       5
     N    1365      2.21       5
     O    1515      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7932
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2408
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2408
          Classifications: {'peptide': 348}
          Incomplete info: {'truncation_to_alanine': 95}
          Link IDs: {'PTRANS': 14, 'TRANS': 333}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 394
          Unresolved non-hydrogen angles: 487
          Unresolved non-hydrogen dihedrals: 342
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLU:plan': 10, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'ASN:plan1': 6, 'TYR:plan': 5, 'GLN:plan1': 9, 'HIS:plan': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 221
    Chain: "A"
      Number of atoms: 3512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 3512
          Classifications: {'peptide': 512}
          Incomplete info: {'truncation_to_alanine': 128}
          Link IDs: {'PTRANS': 25, 'TRANS': 486}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 513
          Unresolved non-hydrogen angles: 638
          Unresolved non-hydrogen dihedrals: 425
          Unresolved non-hydrogen chiralities: 32
          Planarities with less than four sites: {'PHE:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 14, 'GLU:plan': 16, 'ARG:plan': 17, 'TRP:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 8, 'TYR:plan': 4}
          Unresolved non-hydrogen planarities: 321
    Chain: "C"
      Number of atoms: 2010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2010
          Classifications: {'peptide': 269}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 10, 'TRANS': 258}
          Chain breaks: 3
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 177
          Unresolved non-hydrogen angles: 227
          Unresolved non-hydrogen dihedrals: 155
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 110
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.85, per 1000 atoms: 0.23
  Number of scatterers: 7932
  At special positions: 0
  Unit cell: (85.86, 109.18, 121.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Mn      2     24.99
     S      33     16.00
     O    1515      8.00
     N    1365      7.00
     C    5017      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 314.0 milliseconds
  

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2168

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 3 sheets defined
      71.7% alpha, 1.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'B' and resid 161 through 177
    Processing helix  chain 'B' and resid 181 through 189
      removed outlier: 3.608A  pdb=" N   PHE B 185 " --> pdb=" O   PRO B 181 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU B 186 " --> pdb=" O   ASP B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 200
      removed outlier: 4.651A  pdb=" N   GLY B 194 " --> pdb=" O   ASN B 191 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   ASP B 195 " --> pdb=" O   LYS B 192 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   ILE B 197 " --> pdb=" O   GLY B 194 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   LEU B 198 " --> pdb=" O   ASP B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 215
      removed outlier: 4.303A  pdb=" N   ALA B 205 " --> pdb=" O   PRO B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 232
    Processing helix  chain 'B' and resid 233 through 246
    Processing helix  chain 'B' and resid 250 through 267
    Processing helix  chain 'B' and resid 271 through 278
    Processing helix  chain 'B' and resid 292 through 308
      removed outlier: 3.721A  pdb=" N   ASN B 308 " --> pdb=" O   TYR B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 322
    Processing helix  chain 'B' and resid 327 through 336
      removed outlier: 3.569A  pdb=" N   ILE B 331 " --> pdb=" O   GLU B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 360
    Processing helix  chain 'B' and resid 362 through 370
      removed outlier: 3.662A  pdb=" N   ALA B 366 " --> pdb=" O   SER B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 376
      removed outlier: 3.603A  pdb=" N   GLY B 376 " --> pdb=" O   LEU B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 399
      removed outlier: 3.635A  pdb=" N   LEU B 397 " --> pdb=" O   GLU B 393 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASN B 398 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 414
    Processing helix  chain 'B' and resid 417 through 431
      removed outlier: 3.805A  pdb=" N   ILE B 421 " --> pdb=" O   ASP B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 452
      removed outlier: 3.929A  pdb=" N   ALA B 438 " --> pdb=" O   THR B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 463
      removed outlier: 3.718A  pdb=" N   VAL B 459 " --> pdb=" O   LYS B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 492
      removed outlier: 3.723A  pdb=" N   THR B 482 " --> pdb=" O   TRP B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 507
    Processing helix  chain 'B' and resid 508 through 522
      removed outlier: 3.765A  pdb=" N   GLU B 521 " --> pdb=" O   LEU B 517 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ALA B 522 " --> pdb=" O   LYS B 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 525 through 542
    Processing helix  chain 'A' and resid 60 through 74
      removed outlier: 3.903A  pdb=" N   LEU A  64 " --> pdb=" O   ASP A  60 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A  65 " --> pdb=" O   ASP A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 87
    Processing helix  chain 'A' and resid 88 through 98
      removed outlier: 4.221A  pdb=" N   GLU A  92 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 116
      removed outlier: 3.677A  pdb=" N   ARG A 103 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 136
      removed outlier: 4.054A  pdb=" N   HIS A 125 " --> pdb=" O   ASP A 121 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ALA A 135 " --> pdb=" O   LYS A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 153
      removed outlier: 3.951A  pdb=" N   GLY A 147 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   VAL A 148 " --> pdb=" O   SER A 144 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   TYR A 153 " --> pdb=" O   PHE A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 172
      removed outlier: 3.655A  pdb=" N   TYR A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   THR A 169 " --> pdb=" O   ARG A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 194
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 235 through 251
      removed outlier: 3.588A  pdb=" N   GLN A 240 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      Proline residue:  A 244  - end of helix
    Processing helix  chain 'A' and resid 255 through 265
      removed outlier: 4.383A  pdb=" N   ALA A 262 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 271
    Processing helix  chain 'A' and resid 273 through 278
      removed outlier: 3.953A  pdb=" N   THR A 277 " --> pdb=" O   GLY A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 287
    Processing helix  chain 'A' and resid 297 through 308
      removed outlier: 4.315A  pdb=" N   ALA A 301 " --> pdb=" O   ARG A 297 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   GLY A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LYS A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   LYS A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 329
      Proline residue:  A 322  - end of helix
      removed outlier: 3.504A  pdb=" N   SER A 329 " --> pdb=" O   LYS A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 347
      removed outlier: 4.261A  pdb=" N   SER A 341 " --> pdb=" O   SER A 337 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   VAL A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   MET A 344 " --> pdb=" O   ALA A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 365
      removed outlier: 4.216A  pdb=" N   ILE A 356 " --> pdb=" O   LYS A 352 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   GLU A 357 " --> pdb=" O   ASP A 353 " (cutoff:3.500A)
      Proline residue:  A 361  - end of helix
    Processing helix  chain 'A' and resid 366 through 368
      No H-bonds generated for 'chain 'A' and resid 366 through 368'
    Processing helix  chain 'A' and resid 371 through 387
      removed outlier: 3.588A  pdb=" N   LEU A 376 " --> pdb=" O   PRO A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 407
      Proline residue:  A 400  - end of helix
    Processing helix  chain 'A' and resid 412 through 419
      removed outlier: 3.962A  pdb=" N   GLU A 419 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 426
    Processing helix  chain 'A' and resid 436 through 446
      removed outlier: 3.992A  pdb=" N   LEU A 440 " --> pdb=" O   LYS A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 465
      removed outlier: 3.680A  pdb=" N   ASN A 458 " --> pdb=" O   ASP A 454 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ASN A 459 " --> pdb=" O   ALA A 455 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA A 464 " --> pdb=" O   LEU A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 486
      removed outlier: 3.532A  pdb=" N   HIS A 475 " --> pdb=" O   TRP A 471 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   VAL A 477 " --> pdb=" O   MET A 473 " (cutoff:3.500A)
      Proline residue:  A 478  - end of helix
      removed outlier: 4.720A  pdb=" N   GLU A 482 " --> pdb=" O   PRO A 478 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   MET A 483 " --> pdb=" O   GLN A 479 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASN A 485 " --> pdb=" O   LEU A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 503
      removed outlier: 3.524A  pdb=" N   ARG A 492 " --> pdb=" O   HIS A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 524
      removed outlier: 4.218A  pdb=" N   VAL A 518 " --> pdb=" O   LYS A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 539
      removed outlier: 3.521A  pdb=" N   GLN A 539 " --> pdb=" O   ALA A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 564
      Proline residue:  A 556  - end of helix
    Processing helix  chain 'A' and resid 566 through 580
    Processing helix  chain 'C' and resid 5 through 19
    Processing helix  chain 'C' and resid 24 through 42
      removed outlier: 3.596A  pdb=" N   LYS C  41 " --> pdb=" O   GLU C  37 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU C  42 " --> pdb=" O   ILE C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 73
    Processing helix  chain 'C' and resid 92 through 107
      removed outlier: 3.724A  pdb=" N   THR C  96 " --> pdb=" O   TYR C  92 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL C  97 " --> pdb=" O   SER C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 119
    Processing helix  chain 'C' and resid 120 through 125
      removed outlier: 3.900A  pdb=" N   GLN C 125 " --> pdb=" O   ARG C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 153
      removed outlier: 3.927A  pdb=" N   TYR C 152 " --> pdb=" O   ASP C 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 183
    Processing helix  chain 'C' and resid 192 through 201
      removed outlier: 3.815A  pdb=" N   CYS C 196 " --> pdb=" O   GLU C 192 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASP C 197 " --> pdb=" O   GLY C 193 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 233
    Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48
      removed outlier: 3.608A  pdb=" N   ILE C 163 " --> pdb=" O   VAL C 159 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54
      removed outlier: 6.281A  pdb=" N   THR C  53 " --> pdb=" O   LEU C  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 210 through 211

    477 hydrogen bonds defined for protein.
    1413 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: 0.94

  Time building geometry restraints manager: 1.00 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: 1737
        1.33 -     1.45: 1632
        1.45 -     1.57: 4641
        1.57 -     1.70: 0
        1.70 -     1.82: 50
  Bond restraints: 8060
  Sorted by residual:
  bond pdb=" C   TYR A 153 "
       pdb=" N   PRO A 154 "
    ideal  model  delta    sigma   weight residual
    1.333  1.368 -0.035 1.44e-02 4.82e+03 5.83e+00
  bond pdb=" CA  ASN A  57 "
       pdb=" CB  ASN A  57 "
    ideal  model  delta    sigma   weight residual
    1.530  1.554 -0.023 1.69e-02 3.50e+03 1.91e+00
  bond pdb=" N   ASN A  57 "
       pdb=" CA  ASN A  57 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.74e+00
  bond pdb=" C   ILE A 421 "
       pdb=" N   PRO A 422 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 2.34e-02 1.83e+03 1.41e+00
  bond pdb=" C   GLU A 275 "
       pdb=" N   PRO A 276 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.014 1.20e-02 6.94e+03 1.38e+00
  ... (remaining 8055 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 10636
        1.79 -     3.57: 299
        3.57 -     5.36: 69
        5.36 -     7.14: 26
        7.14 -     8.93: 11
  Bond angle restraints: 11041
  Sorted by residual:
  angle pdb=" N   VAL A 549 "
        pdb=" CA  VAL A 549 "
        pdb=" C   VAL A 549 "
      ideal   model   delta    sigma   weight residual
     113.47  105.10    8.37 1.01e+00 9.80e-01 6.86e+01
  angle pdb=" C   ASP A 175 "
        pdb=" CA  ASP A 175 "
        pdb=" CB  ASP A 175 "
      ideal   model   delta    sigma   weight residual
     116.54  110.24    6.30 1.15e+00 7.56e-01 3.00e+01
  angle pdb=" C   ASN A  57 "
        pdb=" CA  ASN A  57 "
        pdb=" CB  ASN A  57 "
      ideal   model   delta    sigma   weight residual
     110.42  118.64   -8.22 1.99e+00 2.53e-01 1.71e+01
  angle pdb=" N   LEU C 186 "
        pdb=" CA  LEU C 186 "
        pdb=" C   LEU C 186 "
      ideal   model   delta    sigma   weight residual
     110.44  115.23   -4.79 1.20e+00 6.94e-01 1.59e+01
  angle pdb=" C   GLN C 187 "
        pdb=" N   GLU C 188 "
        pdb=" CA  GLU C 188 "
      ideal   model   delta    sigma   weight residual
     121.54  129.13   -7.59 1.91e+00 2.74e-01 1.58e+01
  ... (remaining 11036 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 4208
       17.91 -    35.81: 480
       35.81 -    53.72: 109
       53.72 -    71.62: 20
       71.62 -    89.53: 11
  Dihedral angle restraints: 4828
    sinusoidal: 1526
      harmonic: 3302
  Sorted by residual:
  dihedral pdb=" CA  GLN C 187 "
           pdb=" C   GLN C 187 "
           pdb=" N   GLU C 188 "
           pdb=" CA  GLU C 188 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.64   45.36     0      5.00e+00 4.00e-02 8.23e+01
  dihedral pdb=" CA  VAL A 223 "
           pdb=" C   VAL A 223 "
           pdb=" N   GLU A 224 "
           pdb=" CA  GLU A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.38   27.62     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CA  PRO A 177 "
           pdb=" C   PRO A 177 "
           pdb=" N   MET A 178 "
           pdb=" CA  MET A 178 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.83  -25.17     0      5.00e+00 4.00e-02 2.53e+01
  ... (remaining 4825 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 864
       0.032 -    0.065: 345
       0.065 -    0.097: 113
       0.097 -    0.130: 35
       0.130 -    0.162: 9
  Chirality restraints: 1366
  Sorted by residual:
  chirality pdb=" CB  ILE A 421 "
            pdb=" CA  ILE A 421 "
            pdb=" CG1 ILE A 421 "
            pdb=" CG2 ILE A 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.55e-01
  chirality pdb=" CA  ILE C 275 "
            pdb=" N   ILE C 275 "
            pdb=" C   ILE C 275 "
            pdb=" CB  ILE C 275 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.33e-01
  chirality pdb=" CA  PRO B 339 "
            pdb=" N   PRO B 339 "
            pdb=" C   PRO B 339 "
            pdb=" CB  PRO B 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.26e-01
  ... (remaining 1363 not shown)

  Planarity restraints: 1435
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 223 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.04e+00
        pdb=" C   VAL A 223 "    0.035 2.00e-02 2.50e+03
        pdb=" O   VAL A 223 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLU A 224 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 527 "    0.033 5.00e-02 4.00e+02   4.96e-02 3.94e+00
        pdb=" N   PRO A 528 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 528 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 528 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 555 "    0.032 5.00e-02 4.00e+02   4.77e-02 3.64e+00
        pdb=" N   PRO A 556 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 556 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 556 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1432 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 138
        2.65 -     3.21: 8171
        3.21 -     3.77: 13048
        3.77 -     4.34: 16031
        4.34 -     4.90: 25470
  Nonbonded interactions: 62858
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  57 "
            pdb=" N   ASP A  58 "
     model   vdw
     2.084 3.120
  nonbonded pdb=" OD2 ASP C  85 "
            pdb="MN    MN C 401 "
     model   vdw
     2.148 2.320
  nonbonded pdb=" O   LYS C  36 "
            pdb=" OG1 THR C  40 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" OD1 ASP A 392 "
            pdb=" N   LEU A 393 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" O   MET A 159 "
            pdb=" OG1 THR A 162 "
     model   vdw
     2.198 3.040
  ... (remaining 62853 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.000
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.190
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4628
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      :  0.003   0.039   8060  Z= 0.160
  Angle     :  0.803   8.929  11041  Z= 0.438
  Chirality :  0.041   0.162   1366
  Planarity :  0.005   0.050   1435
  Dihedral  : 16.932  89.528   2660
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  9.68 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 31.59 %
    Favored  : 63.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.26), residues: 1095
  helix: -0.05 (0.20), residues: 708
  sheet: -3.56 (0.72), residues: 46
  loop : -2.65 (0.30), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 118 
 TYR   0.015   0.001   TYR A 168 
 PHE   0.029   0.002   PHE C 260 
 TRP   0.026   0.002   TRP A 411 
 HIS   0.006   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8060)
  covalent geometry    : angle       0.80294 (11041)
  hydrogen bonds       : bond        0.14938 (  477)
  hydrogen bonds       : angle       6.84675 ( 1413)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 83
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: B  368 THR cc_start: 0.4309 (p) cc_final: 0.3972 (p)
REVERT: B  515 MET cc_start: 0.1772 (mmt) cc_final: 0.1395 (tpt)
REVERT: A  204 MET cc_start: 0.4663 (ttt) cc_final: 0.3209 (tpt)
REVERT: A  350 LEU cc_start: 0.3623 (OUTLIER) cc_final: 0.2864 (tt)
REVERT: A  405 LEU cc_start: 0.4024 (OUTLIER) cc_final: 0.3517 (mt)
REVERT: A  432 PHE cc_start: 0.3821 (OUTLIER) cc_final: 0.3506 (p90)
REVERT: A  520 MET cc_start: 0.3378 (pp-130) cc_final: 0.2832 (tmm)
REVERT: C   33 GLU cc_start: 0.6029 (mm-30) cc_final: 0.5664 (mm-30)
REVERT: C  113 ILE cc_start: 0.6433 (mt) cc_final: 0.6133 (mt)
REVERT: C  121 ARG cc_start: 0.3122 (OUTLIER) cc_final: 0.1797 (tmm160)
  outliers start: 38
  outliers final: 26
  residues processed: 116
  average time/residue: 0.0752
  time to fit residues: 12.5331
Evaluate side-chains
  108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0970
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.6182

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

Flipped N/Q/H residues before XYZ refinement:
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 GLN
A 236 GLN
A 292 ASN
A 319 HIS
** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  44 ASN
** C  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.179661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.162546 restraints weight = 16782.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.163598 restraints weight = 13468.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.164776 restraints weight = 11144.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.165259 restraints weight = 8734.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.165549 restraints weight = 8327.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.4517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5045
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8060  Z= 0.217
  Angle     :  0.809   9.256  11041  Z= 0.424
  Chirality :  0.047   0.255   1366
  Planarity :  0.006   0.074   1435
  Dihedral  :  6.097  42.824   1163
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.41 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  7.17 %
    Favored  : 92.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.25), residues: 1095
  helix: -0.25 (0.19), residues: 722
  sheet: -4.63 (0.65), residues: 39
  loop : -2.92 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  49 
 TYR   0.015   0.002   TYR C 265 
 PHE   0.024   0.002   PHE A 149 
 TRP   0.026   0.002   TRP B 265 
 HIS   0.014   0.002   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 8060)
  covalent geometry    : angle       0.80925 (11041)
  hydrogen bonds       : bond        0.05021 (  477)
  hydrogen bonds       : angle       5.71713 ( 1413)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 112
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASN cc_start: 0.6311 (t0) cc_final: 0.5578 (t0)
REVERT: A  117 MET cc_start: 0.6972 (tmm) cc_final: 0.6532 (tmm)
REVERT: A  204 MET cc_start: 0.5219 (ttp) cc_final: 0.3656 (tpt)
REVERT: A  350 LEU cc_start: 0.4930 (pt) cc_final: 0.3830 (tt)
REVERT: A  520 MET cc_start: 0.4323 (ppp) cc_final: 0.4070 (tmm)
REVERT: A  551 GLU cc_start: 0.5613 (pm20) cc_final: 0.5196 (mm-30)
REVERT: A  579 SER cc_start: 0.7654 (m) cc_final: 0.7099 (t)
REVERT: C   12 GLN cc_start: 0.6829 (tm-30) cc_final: 0.6114 (mt0)
  outliers start: 3
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0631
  time to fit residues: 10.7869
Evaluate side-chains
  87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 125 HIS
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 450 HIS
A 459 ASN
** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.181654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.166547 restraints weight = 16498.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.166805 restraints weight = 15535.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.168211 restraints weight = 12493.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.168402 restraints weight = 8814.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.168608 restraints weight = 8550.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.4575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4927
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8060  Z= 0.157
  Angle     :  0.710   8.941  11041  Z= 0.367
  Chirality :  0.043   0.203   1366
  Planarity :  0.006   0.065   1435
  Dihedral  :  5.745  39.548   1163
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.59 %
    Favored  : 90.23 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.59 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.25), residues: 1095
  helix: -0.09 (0.20), residues: 724
  sheet: -5.15 (0.69), residues: 29
  loop : -2.85 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 256 
 TYR   0.012   0.001   TYR C 265 
 PHE   0.014   0.002   PHE A 571 
 TRP   0.012   0.002   TRP A 444 
 HIS   0.008   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8060)
  covalent geometry    : angle       0.70984 (11041)
  hydrogen bonds       : bond        0.04458 (  477)
  hydrogen bonds       : angle       5.46732 ( 1413)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.5271 (ttp) cc_final: 0.3700 (tpt)
REVERT: A  350 LEU cc_start: 0.4543 (pt) cc_final: 0.3536 (tt)
REVERT: A  551 GLU cc_start: 0.5475 (pm20) cc_final: 0.5027 (mm-30)
REVERT: C   12 GLN cc_start: 0.6822 (tm-30) cc_final: 0.6052 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0681
  time to fit residues: 11.0180
Evaluate side-chains
  86 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 77 optimal weight:    0.5980
   chunk 52 optimal weight:    7.9990
   chunk 26 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 292 ASN
** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.176034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.165471 restraints weight = 170734.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.168874 restraints weight = 112909.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.167594 restraints weight = 98898.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.167919 restraints weight = 95222.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.167795 restraints weight = 84817.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.4451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5085
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8060  Z= 0.172
  Angle     :  0.718   8.803  11041  Z= 0.375
  Chirality :  0.044   0.227   1366
  Planarity :  0.006   0.064   1435
  Dihedral  :  5.869  38.869   1163
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.14 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  5.38 %
    Favored  : 94.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.25), residues: 1095
  helix: -0.23 (0.19), residues: 740
  sheet: -5.15 (0.69), residues: 31
  loop : -2.76 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  49 
 TYR   0.012   0.002   TYR C 265 
 PHE   0.025   0.002   PHE A 149 
 TRP   0.017   0.002   TRP A 444 
 HIS   0.010   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8060)
  covalent geometry    : angle       0.71789 (11041)
  hydrogen bonds       : bond        0.04460 (  477)
  hydrogen bonds       : angle       5.45826 ( 1413)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.5218 (ttp) cc_final: 0.3914 (tpt)
REVERT: A  350 LEU cc_start: 0.4388 (pt) cc_final: 0.3576 (tt)
REVERT: A  442 MET cc_start: 0.5685 (ppp) cc_final: 0.5426 (ptm)
REVERT: A  551 GLU cc_start: 0.5477 (pm20) cc_final: 0.5026 (mm-30)
REVERT: C   12 GLN cc_start: 0.7475 (tm-30) cc_final: 0.6579 (mt0)
  outliers start: 2
  outliers final: 2
  residues processed: 108
  average time/residue: 0.0708
  time to fit residues: 11.2929
Evaluate side-chains
  87 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 78 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 102 optimal weight:    5.9990
   chunk 110 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 100 optimal weight:    5.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 125 HIS
A 319 HIS
A 410 HIS
** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.177131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.166633 restraints weight = 171440.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.170029 restraints weight = 113921.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.168829 restraints weight = 98275.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.169176 restraints weight = 91696.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.169146 restraints weight = 84204.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.4466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5035
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8060  Z= 0.154
  Angle     :  0.711   8.692  11041  Z= 0.370
  Chirality :  0.043   0.197   1366
  Planarity :  0.005   0.058   1435
  Dihedral  :  5.806  38.712   1163
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.95 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.28 %
    Favored  : 95.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.26), residues: 1095
  helix: -0.05 (0.20), residues: 718
  sheet: -4.53 (0.69), residues: 39
  loop : -2.66 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  49 
 TYR   0.015   0.001   TYR B 232 
 PHE   0.013   0.002   PHE C 289 
 TRP   0.013   0.001   TRP B 449 
 HIS   0.009   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8060)
  covalent geometry    : angle       0.71050 (11041)
  hydrogen bonds       : bond        0.04308 (  477)
  hydrogen bonds       : angle       5.36817 ( 1413)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.5243 (ttp) cc_final: 0.3892 (tpt)
REVERT: A  350 LEU cc_start: 0.4454 (pt) cc_final: 0.3608 (tt)
REVERT: A  575 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7138 (pm20)
REVERT: A  579 SER cc_start: 0.7164 (m) cc_final: 0.6353 (t)
REVERT: C   12 GLN cc_start: 0.7180 (tm-30) cc_final: 0.6585 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0662
  time to fit residues: 10.2039
Evaluate side-chains
  82 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 52 optimal weight:    0.4980
   chunk 49 optimal weight:    0.0370
   chunk 44 optimal weight:    6.9990
   chunk 108 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 0 optimal weight:   30.0000
   chunk 29 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0980
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 533 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.181858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.167087 restraints weight = 16379.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.167543 restraints weight = 15281.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.169094 restraints weight = 11605.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.169268 restraints weight = 8318.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.169451 restraints weight = 7554.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.4588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4896
moved from start:          0.3463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8060  Z= 0.141
  Angle     :  0.697   8.410  11041  Z= 0.362
  Chirality :  0.042   0.205   1366
  Planarity :  0.006   0.083   1435
  Dihedral  :  5.584  38.547   1163
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.50 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.26), residues: 1095
  helix:  0.09 (0.20), residues: 724
  sheet: -4.16 (0.83), residues: 34
  loop : -2.51 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 497 
 TYR   0.015   0.001   TYR C 265 
 PHE   0.016   0.002   PHE B 446 
 TRP   0.021   0.002   TRP A 444 
 HIS   0.007   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8060)
  covalent geometry    : angle       0.69718 (11041)
  hydrogen bonds       : bond        0.04010 (  477)
  hydrogen bonds       : angle       5.17814 ( 1413)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.5311 (ttp) cc_final: 0.3844 (tpt)
REVERT: A  350 LEU cc_start: 0.4767 (pt) cc_final: 0.3815 (tt)
REVERT: A  520 MET cc_start: 0.5386 (tmm) cc_final: 0.5084 (tmm)
REVERT: A  579 SER cc_start: 0.7415 (m) cc_final: 0.6753 (t)
REVERT: C   12 GLN cc_start: 0.6687 (tm-30) cc_final: 0.6132 (mt0)
REVERT: C  113 ILE cc_start: 0.6642 (mt) cc_final: 0.6316 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0671
  time to fit residues: 10.6951
Evaluate side-chains
  83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 73 optimal weight:    0.0270
   chunk 58 optimal weight:    9.9990
   chunk 50 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0020
   chunk 22 optimal weight:    3.9990
   chunk 83 optimal weight:    0.7980
   chunk 68 optimal weight:    6.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.4246

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

Flipped N/Q/H residues before XYZ refinement:
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 GLN
A 450 HIS
** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 533 ASN
** C  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.182811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.168595 restraints weight = 16112.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.168748 restraints weight = 15773.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.170288 restraints weight = 12498.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.170537 restraints weight = 8867.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.170900 restraints weight = 7630.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.4606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4857
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8060  Z= 0.133
  Angle     :  0.677   8.082  11041  Z= 0.349
  Chirality :  0.042   0.198   1366
  Planarity :  0.005   0.071   1435
  Dihedral  :  5.449  38.700   1163
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.50 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.26), residues: 1095
  helix:  0.22 (0.20), residues: 723
  sheet: -4.26 (0.79), residues: 34
  loop : -2.45 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 497 
 TYR   0.014   0.001   TYR C 265 
 PHE   0.017   0.002   PHE B 446 
 TRP   0.020   0.002   TRP A 411 
 HIS   0.008   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8060)
  covalent geometry    : angle       0.67704 (11041)
  hydrogen bonds       : bond        0.03785 (  477)
  hydrogen bonds       : angle       5.05114 ( 1413)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.5297 (ttp) cc_final: 0.3851 (tpt)
REVERT: A  350 LEU cc_start: 0.4654 (pt) cc_final: 0.3783 (tt)
REVERT: A  579 SER cc_start: 0.7370 (m) cc_final: 0.6454 (t)
REVERT: C   12 GLN cc_start: 0.6686 (tm-30) cc_final: 0.6142 (mt0)
REVERT: C  113 ILE cc_start: 0.6245 (mt) cc_final: 0.6005 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0694
  time to fit residues: 10.0497
Evaluate side-chains
  81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 57 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 86 optimal weight:    0.5980
   chunk 87 optimal weight:    0.7980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 533 ASN
** C  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.177632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.163661 restraints weight = 17574.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.163247 restraints weight = 20322.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.164769 restraints weight = 16541.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.164947 restraints weight = 11483.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.165079 restraints weight = 11164.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.4520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4999
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8060  Z= 0.167
  Angle     :  0.731   8.330  11041  Z= 0.381
  Chirality :  0.044   0.194   1366
  Planarity :  0.006   0.065   1435
  Dihedral  :  5.699  43.584   1163
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.14 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.26), residues: 1095
  helix:  0.01 (0.20), residues: 728
  sheet: -4.77 (0.75), residues: 31
  loop : -2.51 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  49 
 TYR   0.013   0.001   TYR C 265 
 PHE   0.022   0.002   PHE A 149 
 TRP   0.014   0.002   TRP B 449 
 HIS   0.010   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8060)
  covalent geometry    : angle       0.73123 (11041)
  hydrogen bonds       : bond        0.04168 (  477)
  hydrogen bonds       : angle       5.24276 ( 1413)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.5410 (ttp) cc_final: 0.3880 (tpt)
REVERT: A  350 LEU cc_start: 0.5001 (pt) cc_final: 0.4184 (tt)
REVERT: A  579 SER cc_start: 0.7371 (m) cc_final: 0.6410 (t)
REVERT: C   12 GLN cc_start: 0.6648 (tm-30) cc_final: 0.6199 (mt0)
REVERT: C  148 ASP cc_start: 0.7687 (m-30) cc_final: 0.6765 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0674
  time to fit residues: 10.1663
Evaluate side-chains
  81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0870
   chunk 13 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN
** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 533 ASN
** C  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.179115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.165650 restraints weight = 17568.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.165048 restraints weight = 19582.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.166366 restraints weight = 17238.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.166100 restraints weight = 13448.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.166611 restraints weight = 11380.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.4539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4957
moved from start:          0.3942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8060  Z= 0.149
  Angle     :  0.712   8.680  11041  Z= 0.371
  Chirality :  0.043   0.189   1366
  Planarity :  0.005   0.061   1435
  Dihedral  :  5.545  41.774   1163
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.95 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.26), residues: 1095
  helix:  0.07 (0.20), residues: 734
  sheet: -4.38 (0.78), residues: 31
  loop : -2.48 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  49 
 TYR   0.014   0.001   TYR C 265 
 PHE   0.018   0.002   PHE B 446 
 TRP   0.012   0.001   TRP A 411 
 HIS   0.009   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8060)
  covalent geometry    : angle       0.71230 (11041)
  hydrogen bonds       : bond        0.03983 (  477)
  hydrogen bonds       : angle       5.19202 ( 1413)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.5670 (ttp) cc_final: 0.4045 (tpt)
REVERT: A  350 LEU cc_start: 0.5006 (pt) cc_final: 0.4263 (tt)
REVERT: A  579 SER cc_start: 0.7330 (m) cc_final: 0.6410 (t)
REVERT: C   12 GLN cc_start: 0.6587 (tm-30) cc_final: 0.6161 (mt0)
REVERT: C  286 PHE cc_start: 0.6784 (m-80) cc_final: 0.6566 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0724
  time to fit residues: 10.9315
Evaluate side-chains
  78 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 94 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9980
   chunk 83 optimal weight:    0.2980
   chunk 76 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 34 optimal weight:   20.0000
   chunk 57 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 533 ASN
A 574 ASN
** C  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.178997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.165247 restraints weight = 17567.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.164978 restraints weight = 18409.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.166611 restraints weight = 14532.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.166481 restraints weight = 10616.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.166748 restraints weight = 9594.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.4542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4952
moved from start:          0.4093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8060  Z= 0.148
  Angle     :  0.722   9.012  11041  Z= 0.374
  Chirality :  0.043   0.189   1366
  Planarity :  0.005   0.059   1435
  Dihedral  :  5.506  41.930   1163
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.77 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.26), residues: 1095
  helix:  0.06 (0.20), residues: 737
  sheet: -4.43 (0.78), residues: 31
  loop : -2.44 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 239 
 TYR   0.015   0.001   TYR C 265 
 PHE   0.018   0.002   PHE B 446 
 TRP   0.021   0.002   TRP B 297 
 HIS   0.009   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8060)
  covalent geometry    : angle       0.72215 (11041)
  hydrogen bonds       : bond        0.03927 (  477)
  hydrogen bonds       : angle       5.15684 ( 1413)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.5713 (ttp) cc_final: 0.4033 (tpt)
REVERT: A  350 LEU cc_start: 0.5261 (pt) cc_final: 0.4468 (tt)
REVERT: A  407 GLU cc_start: 0.6958 (pm20) cc_final: 0.6141 (pm20)
REVERT: A  579 SER cc_start: 0.7348 (m) cc_final: 0.6464 (t)
REVERT: C   12 GLN cc_start: 0.6773 (tm-30) cc_final: 0.6222 (mt0)
REVERT: C   33 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6446 (mm-30)
REVERT: C  113 ILE cc_start: 0.6528 (mt) cc_final: 0.6236 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0695
  time to fit residues: 10.2712
Evaluate side-chains
  81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 70 optimal weight:    0.4980
   chunk 93 optimal weight:    3.9990
   chunk 102 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0060
   chunk 107 optimal weight:    0.0970
   chunk 15 optimal weight:    4.9990
   chunk 99 optimal weight:    0.2980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.3194

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

Flipped N/Q/H residues before XYZ refinement:
** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 533 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.181739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.166118 restraints weight = 17227.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.166719 restraints weight = 15784.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.167321 restraints weight = 13323.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.167527 restraints weight = 11313.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.167705 restraints weight = 10615.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.4547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4905
moved from start:          0.4208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8060  Z= 0.137
  Angle     :  0.706   8.656  11041  Z= 0.364
  Chirality :  0.043   0.193   1366
  Planarity :  0.005   0.056   1435
  Dihedral  :  5.307  42.216   1163
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.13 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.26), residues: 1095
  helix:  0.23 (0.20), residues: 734
  sheet: -4.19 (0.83), residues: 34
  loop : -2.39 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  49 
 TYR   0.018   0.001   TYR C 265 
 PHE   0.018   0.002   PHE B 446 
 TRP   0.023   0.002   TRP C  13 
 HIS   0.007   0.001   HIS C 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8060)
  covalent geometry    : angle       0.70641 (11041)
  hydrogen bonds       : bond        0.03734 (  477)
  hydrogen bonds       : angle       5.01161 ( 1413)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1309.25 seconds
wall clock time: 23 minutes 14.10 seconds (1394.10 seconds total)