Starting phenix.real_space_refine
on Thu Mar 13 18:17:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zde_14643/03_2025/7zde_14643_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zde_14643/03_2025/7zde_14643.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zde_14643/03_2025/7zde_14643.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zde_14643/03_2025/7zde_14643.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zde_14643/03_2025/7zde_14643_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zde_14643/03_2025/7zde_14643_neut.cif"
  }
  resolution = 3.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      28      5.16       5
     C    5771      2.51       5
     N    1586      2.21       5
     O    1625      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 94 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9014
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 4418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4418
          Classifications: {'peptide': 572}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 18, 'TRANS': 553}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "D"
      Number of atoms: 4564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4564
          Classifications: {'peptide': 587}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 27, 'TRANS': 559}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 15
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.07, per 1000 atoms: 0.67
  Number of scatterers: 9014
  At special positions: 0
  Unit cell: (125.55, 75.33, 112.995, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      28     16.00
     P       3     15.00
     Mg      1     11.99
     O    1625      8.00
     N    1586      7.00
     C    5771      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.22
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 6 sheets defined
      66.5% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'C' and resid 1 through 3
      No H-bonds generated for 'chain 'C' and resid 1 through 3'
    Processing helix  chain 'C' and resid 4 through 9
    Processing helix  chain 'C' and resid 10 through 13
      removed outlier: 3.694A  pdb=" N   ARG C  13 " --> pdb=" O   LEU C  10 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 10 through 13'
    Processing helix  chain 'C' and resid 14 through 50
      removed outlier: 3.502A  pdb=" N   ALA C  25 " --> pdb=" O   GLY C  21 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU C  29 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU C  36 " --> pdb=" O   SER C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 54
    Processing helix  chain 'C' and resid 59 through 104
      removed outlier: 3.528A  pdb=" N   ARG C  67 " --> pdb=" O   ALA C  63 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ARG C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG C  77 " --> pdb=" O   ARG C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 131
    Processing helix  chain 'C' and resid 132 through 134
      No H-bonds generated for 'chain 'C' and resid 132 through 134'
    Processing helix  chain 'C' and resid 137 through 156
      removed outlier: 3.619A  pdb=" N   VAL C 150 " --> pdb=" O   VAL C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 176
    Processing helix  chain 'C' and resid 176 through 185
    Processing helix  chain 'C' and resid 186 through 209
      removed outlier: 3.823A  pdb=" N   GLY C 197 " --> pdb=" O   THR C 193 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 216
      removed outlier: 3.540A  pdb=" N   ILE C 215 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 218 through 268
      removed outlier: 3.907A  pdb=" N   THR C 224 " --> pdb=" O   ASP C 220 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLN C 225 " --> pdb=" O   ARG C 221 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLN C 240 " --> pdb=" O   ALA C 236 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU C 246 " --> pdb=" O   GLU C 242 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL C 259 " --> pdb=" O   GLY C 255 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER C 267 " --> pdb=" O   LEU C 263 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLY C 268 " --> pdb=" O   TRP C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 291
      removed outlier: 3.588A  pdb=" N   LEU C 282 " --> pdb=" O   ALA C 278 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   PHE C 283 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   PHE C 291 " --> pdb=" O   ALA C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 293
      No H-bonds generated for 'chain 'C' and resid 292 through 293'
    Processing helix  chain 'C' and resid 294 through 295
      No H-bonds generated for 'chain 'C' and resid 294 through 295'
    Processing helix  chain 'C' and resid 296 through 303
    Processing helix  chain 'C' and resid 303 through 319
    Processing helix  chain 'C' and resid 381 through 386
    Processing helix  chain 'C' and resid 403 through 407
    Processing helix  chain 'C' and resid 408 through 413
    Processing helix  chain 'C' and resid 429 through 435
    Processing helix  chain 'C' and resid 442 through 453
    Processing helix  chain 'C' and resid 455 through 460
      removed outlier: 3.937A  pdb=" N   GLU C 460 " --> pdb=" O   LYS C 457 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 466
    Processing helix  chain 'C' and resid 479 through 491
    Processing helix  chain 'C' and resid 506 through 521
      removed outlier: 3.710A  pdb=" N   SER C 511 " --> pdb=" O   ALA C 507 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   GLN C 512 " --> pdb=" O   THR C 508 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU C 519 " --> pdb=" O   GLU C 515 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 535 through 539
      removed outlier: 3.610A  pdb=" N   ARG C 538 " --> pdb=" O   GLY C 535 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 555 through 562
      removed outlier: 3.703A  pdb=" N   ARG C 562 " --> pdb=" O   GLU C 558 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 564 through 571
    Processing helix  chain 'D' and resid 3 through 14
      removed outlier: 3.684A  pdb=" N   GLU D   8 " --> pdb=" O   SER D   4 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 15 through 19
      removed outlier: 3.604A  pdb=" N   VAL D  18 " --> pdb=" O   GLN D  15 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE D  19 " --> pdb=" O   GLN D  16 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 15 through 19'
    Processing helix  chain 'D' and resid 21 through 54
      removed outlier: 3.539A  pdb=" N   ARG D  28 " --> pdb=" O   LEU D  24 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ILE D  39 " --> pdb=" O   GLY D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 61
    Processing helix  chain 'D' and resid 62 through 109
      removed outlier: 3.602A  pdb=" N   ILE D  94 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA D  97 " --> pdb=" O   HIS D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 115
      removed outlier: 4.028A  pdb=" N   TRP D 113 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLN D 115 " --> pdb=" O   PRO D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 127
      removed outlier: 3.509A  pdb=" N   ALA D 123 " --> pdb=" O   ALA D 119 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LEU D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 127 through 132
    Processing helix  chain 'D' and resid 133 through 139
      removed outlier: 3.919A  pdb=" N   TYR D 137 " --> pdb=" O   MET D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 159
      removed outlier: 3.919A  pdb=" N   VAL D 148 " --> pdb=" O   MET D 144 " (cutoff:3.500A)
      Proline residue:  D 151  - end of helix
    Processing helix  chain 'D' and resid 162 through 185
      removed outlier: 3.575A  pdb=" N   ALA D 166 " --> pdb=" O   ASN D 162 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU D 169 " --> pdb=" O   ALA D 165 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   THR D 172 " --> pdb=" O   ILE D 168 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ALA D 173 " --> pdb=" O   LEU D 169 " (cutoff:3.500A)
      Proline residue:  D 174  - end of helix
      Proline residue:  D 177  - end of helix
    Processing helix  chain 'D' and resid 194 through 201
    Processing helix  chain 'D' and resid 203 through 211
    Processing helix  chain 'D' and resid 211 through 218
    Processing helix  chain 'D' and resid 224 through 274
      removed outlier: 3.531A  pdb=" N   PHE D 235 " --> pdb=" O   ALA D 231 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLU D 241 " --> pdb=" O   GLN D 237 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL D 242 " --> pdb=" O   ARG D 238 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU D 245 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   LEU D 248 " --> pdb=" O   ARG D 244 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU D 253 " --> pdb=" O   SER D 249 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLU D 254 " --> pdb=" O   SER D 250 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 311
      removed outlier: 3.631A  pdb=" N   ALA D 293 " --> pdb=" O   ALA D 289 " (cutoff:3.500A)
      Proline residue:  D 298  - end of helix
      removed outlier: 3.947A  pdb=" N   PHE D 301 " --> pdb=" O   ALA D 297 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
      removed outlier: 3.555A  pdb=" N   GLY D 308 " --> pdb=" O   LEU D 304 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   THR D 309 " --> pdb=" O   ARG D 305 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 311 through 329
      removed outlier: 3.643A  pdb=" N   ALA D 315 " --> pdb=" O   TYR D 311 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   SER D 323 " --> pdb=" O   GLY D 319 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 388 through 397
      removed outlier: 3.638A  pdb=" N   LEU D 392 " --> pdb=" O   GLY D 388 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU D 393 " --> pdb=" O   LYS D 389 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 417 through 422
    Processing helix  chain 'D' and resid 438 through 444
    Processing helix  chain 'D' and resid 451 through 462
      removed outlier: 3.527A  pdb=" N   ALA D 462 " --> pdb=" O   ALA D 458 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 487 through 500
      removed outlier: 3.697A  pdb=" N   ARG D 493 " --> pdb=" O   GLY D 489 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL D 494 " --> pdb=" O   GLN D 490 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA D 495 " --> pdb=" O   ALA D 491 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 517 through 532
      removed outlier: 3.528A  pdb=" N   GLN D 522 " --> pdb=" O   ALA D 518 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA D 527 " --> pdb=" O   ARG D 523 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 566 through 572
      removed outlier: 3.528A  pdb=" N   LEU D 570 " --> pdb=" O   ARG D 566 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   VAL D 572 " --> pdb=" O   ALA D 568 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 575 through 587
      removed outlier: 3.795A  pdb=" N   GLU D 587 " --> pdb=" O   HIS D 583 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 339 through 342
    Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419
      removed outlier: 6.476A  pdb=" N   VAL C 496 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   VAL C 529 " --> pdb=" O   VAL C 496 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   LEU C 498 " --> pdb=" O   VAL C 529 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ILE C 369 " --> pdb=" O   MET C 528 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   THR C 530 " --> pdb=" O   ILE C 369 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ILE C 371 " --> pdb=" O   THR C 530 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   ILE C 542 " --> pdb=" O   GLN C 553 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   GLN C 553 " --> pdb=" O   ILE C 542 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   VAL C 544 " --> pdb=" O   ILE C 551 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE C 551 " --> pdb=" O   VAL C 544 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASP C 546 " --> pdb=" O   GLN C 549 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 370 through 372
    Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 366
      removed outlier: 6.507A  pdb=" N   ILE D 357 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER D 401 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 379 through 381
      removed outlier: 6.157A  pdb=" N   LEU D 507 " --> pdb=" O   LEU D 538 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   VAL D 540 " --> pdb=" O   LEU D 507 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   LEU D 509 " --> pdb=" O   VAL D 540 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER D 426 " --> pdb=" O   LEU D 506 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 555 through 557
      removed outlier: 7.070A  pdb=" N   VAL D 555 " --> pdb=" O   ILE D 562 " (cutoff:3.500A)

    508 hydrogen bonds defined for protein.
    1476 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.67

  Time building geometry restraints manager: 2.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2973
        1.34 -     1.45: 1172
        1.45 -     1.57: 4986
        1.57 -     1.69: 6
        1.69 -     1.80: 54
  Bond restraints: 9191
  Sorted by residual:
  bond pdb=" N3B ANP D 602 "
       pdb=" PG  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.795  1.625  0.170 2.00e-02 2.50e+03 7.24e+01
  bond pdb=" O3A ANP D 602 "
       pdb=" PB  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.700  1.594  0.106 2.00e-02 2.50e+03 2.83e+01
  bond pdb=" N   SER C 476 "
       pdb=" CA  SER C 476 "
    ideal  model  delta    sigma   weight residual
    1.452  1.487 -0.035 1.25e-02 6.40e+03 7.64e+00
  bond pdb=" O5' ANP D 602 "
       pdb=" PA  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.655  1.600  0.055 2.00e-02 2.50e+03 7.53e+00
  bond pdb=" N   ARG C 374 "
       pdb=" CA  ARG C 374 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 1.31e-02 5.83e+03 7.26e+00
  ... (remaining 9186 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 12151
        1.98 -     3.96: 279
        3.96 -     5.93: 49
        5.93 -     7.91: 8
        7.91 -     9.89: 5
  Bond angle restraints: 12492
  Sorted by residual:
  angle pdb=" N   GLU C 479 "
        pdb=" CA  GLU C 479 "
        pdb=" C   GLU C 479 "
      ideal   model   delta    sigma   weight residual
     112.68  104.06    8.62 1.33e+00 5.65e-01 4.20e+01
  angle pdb=" N   PRO D 448 "
        pdb=" CA  PRO D 448 "
        pdb=" CB  PRO D 448 "
      ideal   model   delta    sigma   weight residual
     103.33  109.86   -6.53 1.10e+00 8.26e-01 3.52e+01
  angle pdb=" C   ASN C 400 "
        pdb=" N   ASP C 401 "
        pdb=" CA  ASP C 401 "
      ideal   model   delta    sigma   weight residual
     121.54  128.48   -6.94 1.91e+00 2.74e-01 1.32e+01
  angle pdb=" N   ARG D 192 "
        pdb=" CA  ARG D 192 "
        pdb=" C   ARG D 192 "
      ideal   model   delta    sigma   weight residual
     112.93  108.18    4.75 1.33e+00 5.65e-01 1.28e+01
  angle pdb=" CA  LYS C 379 "
        pdb=" C   LYS C 379 "
        pdb=" O   LYS C 379 "
      ideal   model   delta    sigma   weight residual
     121.84  117.93    3.91 1.16e+00 7.43e-01 1.13e+01
  ... (remaining 12487 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.63: 5034
       19.63 -    39.26: 394
       39.26 -    58.90: 43
       58.90 -    78.53: 15
       78.53 -    98.16: 12
  Dihedral angle restraints: 5498
    sinusoidal: 2174
      harmonic: 3324
  Sorted by residual:
  dihedral pdb=" CA  ARG D 422 "
           pdb=" C   ARG D 422 "
           pdb=" N   LYS D 423 "
           pdb=" CA  LYS D 423 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.51   18.49     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" O2' ANP D 602 "
           pdb=" C2' ANP D 602 "
           pdb=" C3' ANP D 602 "
           pdb=" O3' ANP D 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.90  -50.26   98.16     1      3.00e+01 1.11e-03 1.22e+01
  dihedral pdb=" C1' ANP D 602 "
           pdb=" C2' ANP D 602 "
           pdb=" C3' ANP D 602 "
           pdb=" O3' ANP D 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     164.59   70.84   93.75     1      3.00e+01 1.11e-03 1.14e+01
  ... (remaining 5495 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1332
       0.077 -    0.155: 111
       0.155 -    0.232: 10
       0.232 -    0.309: 0
       0.309 -    0.386: 1
  Chirality restraints: 1454
  Sorted by residual:
  chirality pdb=" C3' ANP D 602 "
            pdb=" C2' ANP D 602 "
            pdb=" C4' ANP D 602 "
            pdb=" O3' ANP D 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.74    0.39 2.00e-01 2.50e+01 3.73e+00
  chirality pdb=" CA  PRO D 448 "
            pdb=" N   PRO D 448 "
            pdb=" C   PRO D 448 "
            pdb=" CB  PRO D 448 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" C4' ANP D 602 "
            pdb=" C3' ANP D 602 "
            pdb=" C5' ANP D 602 "
            pdb=" O4' ANP D 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.65    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1451 not shown)

  Planarity restraints: 1593
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 427 "    0.018 2.00e-02 2.50e+03   2.43e-02 1.47e+01
        pdb=" CG  TRP D 427 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 427 "    0.042 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 427 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 427 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 427 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 427 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 427 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 427 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 427 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 419 "   -0.037 5.00e-02 4.00e+02   5.62e-02 5.06e+00
        pdb=" N   PRO C 420 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO C 420 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 420 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 178 "    0.033 5.00e-02 4.00e+02   4.94e-02 3.91e+00
        pdb=" N   PRO C 179 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO C 179 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 179 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1590 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 96
        2.63 -     3.20: 8284
        3.20 -     3.77: 13693
        3.77 -     4.33: 19889
        4.33 -     4.90: 32580
  Nonbonded interactions: 74542
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN D 377 "
            pdb=" OD2 ASP D 551 "
     model   vdw
     2.067 3.120
  nonbonded pdb=" OG  SER D 417 "
            pdb=" OG  SER D 420 "
     model   vdw
     2.122 3.040
  nonbonded pdb=" NE1 TRP D 463 "
            pdb=" OE2 GLU D 526 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" NE2 GLN C 345 "
            pdb=" O   THR C 347 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" OG  SER D 390 "
            pdb="MG    MG D 601 "
     model   vdw
     2.227 2.170
  ... (remaining 74537 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.630
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
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      :  0.008   0.170   9191  Z= 0.501
  Angle     :  0.777   9.891  12492  Z= 0.431
  Chirality :  0.047   0.386   1454
  Planarity :  0.004   0.056   1593
  Dihedral  : 14.795  98.162   3354
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.23), residues: 1153
  helix: -2.34 (0.17), residues: 685
  sheet: -0.75 (0.75), residues: 61
  loop : -1.12 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP D 427 
 HIS   0.005   0.001   HIS C 531 
 PHE   0.016   0.002   PHE D  66 
 TYR   0.014   0.002   TYR D  88 
 ARG   0.008   0.001   ARG D  85 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.205 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8396 (mptt)
REVERT: C  545 MET cc_start: 0.7939 (tpt) cc_final: 0.7511 (tpt)
REVERT: D   15 GLN cc_start: 0.8232 (tm-30) cc_final: 0.8021 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.3300
  time to fit residues: 49.9994
Evaluate side-chains
  102 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.5980
   chunk 87 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 104 optimal weight:    8.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
C 248 GLN
C 421 GLN
C 549 GLN
D 115 GLN
D 377 GLN
D 543 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.145266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.100271 restraints weight = 10395.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 1.55
r_work: 0.2794 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9191  Z= 0.226
  Angle     :  0.623  10.335  12492  Z= 0.312
  Chirality :  0.041   0.187   1454
  Planarity :  0.005   0.054   1593
  Dihedral  :  7.185  56.739   1293
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  7.30 %
    Favored  : 92.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.24), residues: 1153
  helix: -0.72 (0.19), residues: 698
  sheet: -0.89 (0.72), residues: 61
  loop : -1.02 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 427 
 HIS   0.003   0.001   HIS C 132 
 PHE   0.008   0.001   PHE D 327 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.005   0.000   ARG D 192 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 120
  time to evaluate  : 0.916 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8397 (mmtt)
REVERT: C  431 ARG cc_start: 0.8001 (mtp85) cc_final: 0.7764 (mtp-110)
REVERT: C  545 MET cc_start: 0.8293 (tpt) cc_final: 0.7988 (tpt)
REVERT: D   15 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8473 (tp-100)
REVERT: D  115 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8363 (pt0)
  outliers start: 3
  outliers final: 1
  residues processed: 122
  average time/residue: 0.2759
  time to fit residues: 44.3127
Evaluate side-chains
  105 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  315 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 100 optimal weight:    0.2980
   chunk 13 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 549 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.145989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.100129 restraints weight = 10413.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 1.65
r_work: 0.2822 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2684 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   9191  Z= 0.205
  Angle     :  0.558   9.955  12492  Z= 0.276
  Chirality :  0.039   0.145   1454
  Planarity :  0.004   0.049   1593
  Dihedral  :  5.561  50.984   1293
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.41 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.25), residues: 1153
  helix:  0.46 (0.20), residues: 689
  sheet: -1.16 (0.68), residues: 61
  loop : -0.96 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C 368 
 PHE   0.010   0.001   PHE C 181 
 TYR   0.019   0.001   TYR D  88 
 ARG   0.005   0.000   ARG C 452 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8302 (mmtt)
REVERT: C  451 ARG cc_start: 0.9044 (ttm110) cc_final: 0.8380 (mtm-85)
REVERT: C  452 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7784 (ttp80)
REVERT: C  549 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7113 (mp10)
REVERT: D   15 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8483 (tp-100)
REVERT: D  115 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8330 (pt0)
REVERT: D  329 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7463 (pt0)
  outliers start: 8
  outliers final: 5
  residues processed: 118
  average time/residue: 0.2769
  time to fit residues: 43.1670
Evaluate side-chains
  114 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain C residue  549 GLN
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  494 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 107 optimal weight:    0.8980
   chunk 83 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 108 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
C 208 GLN
C 345 GLN
C 549 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.145125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.098700 restraints weight = 10377.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 1.64
r_work: 0.2815 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2681 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9191  Z= 0.234
  Angle     :  0.549   9.539  12492  Z= 0.272
  Chirality :  0.040   0.145   1454
  Planarity :  0.004   0.049   1593
  Dihedral  :  5.209  59.782   1293
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.70 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.25), residues: 1153
  helix:  0.86 (0.20), residues: 688
  sheet: -1.23 (0.65), residues: 61
  loop : -0.91 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C  85 
 PHE   0.010   0.001   PHE C 181 
 TYR   0.020   0.001   TYR D  88 
 ARG   0.004   0.000   ARG D 192 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8312 (mmtt)
REVERT: C  444 GLU cc_start: 0.8333 (tt0) cc_final: 0.7919 (tm-30)
REVERT: C  451 ARG cc_start: 0.9067 (ttm110) cc_final: 0.8426 (mtm-85)
REVERT: C  549 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7764 (mp10)
REVERT: D   15 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8481 (tp-100)
REVERT: D  115 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8350 (pt0)
REVERT: D  329 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7469 (pt0)
  outliers start: 15
  outliers final: 10
  residues processed: 125
  average time/residue: 0.2526
  time to fit residues: 42.3266
Evaluate side-chains
  121 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 MET
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain C residue  549 GLN
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  355 LEU
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  536 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 105 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0770
   chunk 54 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
C 237 GLN
C 549 GLN
D 204 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.146515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.100670 restraints weight = 10345.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.58
r_work: 0.2860 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   9191  Z= 0.193
  Angle     :  0.523   9.122  12492  Z= 0.259
  Chirality :  0.039   0.143   1454
  Planarity :  0.004   0.046   1593
  Dihedral  :  4.900  53.073   1293
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.09 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.25), residues: 1153
  helix:  1.19 (0.20), residues: 691
  sheet: -1.10 (0.60), residues: 71
  loop : -0.91 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  81 
 HIS   0.002   0.001   HIS C  85 
 PHE   0.009   0.001   PHE C 181 
 TYR   0.020   0.001   TYR D  88 
 ARG   0.004   0.000   ARG D 192 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 1.474 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8334 (mmtt)
REVERT: C  444 GLU cc_start: 0.8273 (tt0) cc_final: 0.7921 (tm-30)
REVERT: C  451 ARG cc_start: 0.9077 (ttm110) cc_final: 0.8459 (mtm-85)
REVERT: C  452 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7769 (ttp80)
REVERT: C  519 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7400 (pm20)
REVERT: C  549 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7610 (mp10)
REVERT: D   15 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8469 (tp-100)
REVERT: D  329 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7466 (pt0)
REVERT: D  511 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7807 (mt-10)
  outliers start: 14
  outliers final: 8
  residues processed: 123
  average time/residue: 0.2904
  time to fit residues: 48.6635
Evaluate side-chains
  118 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 MET
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  519 GLU
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain C residue  549 GLN
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  511 GLU
Chi-restraints excluded: chain D residue  536 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 112 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
C 549 GLN
D 557 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.145302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.099690 restraints weight = 10251.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 1.57
r_work: 0.2866 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2734 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9191  Z= 0.219
  Angle     :  0.527   9.408  12492  Z= 0.261
  Chirality :  0.040   0.143   1454
  Planarity :  0.004   0.047   1593
  Dihedral  :  4.784  50.783   1293
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.20 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.25), residues: 1153
  helix:  1.28 (0.20), residues: 690
  sheet: -1.39 (0.68), residues: 56
  loop : -0.94 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  81 
 HIS   0.003   0.001   HIS D 204 
 PHE   0.010   0.001   PHE C 181 
 TYR   0.020   0.001   TYR D  88 
 ARG   0.007   0.000   ARG D 407 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.998 
Fit side-chains
REVERT: C   12 LYS cc_start: 0.9077 (ttmt) cc_final: 0.8323 (mmtt)
REVERT: C  444 GLU cc_start: 0.8330 (tt0) cc_final: 0.7919 (tm-30)
REVERT: C  451 ARG cc_start: 0.9057 (ttm110) cc_final: 0.8464 (mtm-85)
REVERT: C  452 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7857 (ttp80)
REVERT: C  519 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7322 (pm20)
REVERT: C  549 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7690 (mp10)
REVERT: D   15 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8493 (tp-100)
REVERT: D  329 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7427 (pt0)
REVERT: D  389 LYS cc_start: 0.8359 (mtmm) cc_final: 0.7703 (mtmm)
REVERT: D  511 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7831 (mt-10)
  outliers start: 20
  outliers final: 11
  residues processed: 125
  average time/residue: 0.2981
  time to fit residues: 50.9230
Evaluate side-chains
  122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 MET
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  519 GLU
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain C residue  549 GLN
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  355 LEU
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  511 GLU
Chi-restraints excluded: chain D residue  536 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 70 optimal weight:    0.5980
   chunk 69 optimal weight:    0.3980
   chunk 111 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 421 GLN
C 549 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.146407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.099828 restraints weight = 10529.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 1.66
r_work: 0.2837 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9191  Z= 0.195
  Angle     :  0.524   9.736  12492  Z= 0.258
  Chirality :  0.039   0.143   1454
  Planarity :  0.004   0.045   1593
  Dihedral  :  4.678  51.018   1293
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.63 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.25), residues: 1153
  helix:  1.46 (0.20), residues: 691
  sheet: -1.30 (0.68), residues: 56
  loop : -0.90 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 427 
 HIS   0.003   0.001   HIS D 204 
 PHE   0.009   0.001   PHE C 181 
 TYR   0.020   0.001   TYR D  88 
 ARG   0.004   0.000   ARG D 192 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.9051 (ttmt) cc_final: 0.8290 (mmtt)
REVERT: C  444 GLU cc_start: 0.8337 (tt0) cc_final: 0.7923 (tm-30)
REVERT: C  451 ARG cc_start: 0.9045 (ttm110) cc_final: 0.8461 (mtm-85)
REVERT: C  452 ARG cc_start: 0.8254 (ttp80) cc_final: 0.8011 (mtm180)
REVERT: C  519 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7304 (pm20)
REVERT: C  549 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7611 (mp10)
REVERT: D   15 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8484 (tp-100)
REVERT: D  117 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8192 (mtpt)
REVERT: D  329 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7382 (pt0)
REVERT: D  350 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.7920 (mt)
REVERT: D  427 TRP cc_start: 0.7355 (p-90) cc_final: 0.6981 (p-90)
REVERT: D  511 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7806 (mt-10)
  outliers start: 19
  outliers final: 11
  residues processed: 126
  average time/residue: 0.2672
  time to fit residues: 44.9400
Evaluate side-chains
  127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 MET
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  519 GLU
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain C residue  545 MET
Chi-restraints excluded: chain C residue  549 GLN
Chi-restraints excluded: chain D residue  345 THR
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  511 GLU
Chi-restraints excluded: chain D residue  536 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 90 optimal weight:    0.3980
   chunk 91 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0670
   chunk 17 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 38 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
C 549 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.147554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.100859 restraints weight = 10448.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 1.69
r_work: 0.2877 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2741 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   9191  Z= 0.175
  Angle     :  0.523   9.903  12492  Z= 0.254
  Chirality :  0.038   0.143   1454
  Planarity :  0.003   0.044   1593
  Dihedral  :  4.554  50.133   1293
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.16 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.25), residues: 1153
  helix:  1.67 (0.20), residues: 692
  sheet: -1.16 (0.64), residues: 66
  loop : -0.84 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  81 
 HIS   0.003   0.001   HIS D 204 
 PHE   0.008   0.001   PHE C 181 
 TYR   0.019   0.001   TYR D  88 
 ARG   0.004   0.000   ARG D 192 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8333 (mmtt)
REVERT: C  451 ARG cc_start: 0.9025 (ttm110) cc_final: 0.8470 (mtm110)
REVERT: C  519 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7300 (pm20)
REVERT: C  549 GLN cc_start: 0.8008 (mp-120) cc_final: 0.7520 (mp10)
REVERT: D   15 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8528 (tp-100)
REVERT: D  117 LYS cc_start: 0.8369 (mtmt) cc_final: 0.8143 (mtpt)
REVERT: D  329 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7404 (pt0)
REVERT: D  350 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8062 (mt)
REVERT: D  389 LYS cc_start: 0.8333 (mtmm) cc_final: 0.7757 (mtmm)
REVERT: D  427 TRP cc_start: 0.7396 (p-90) cc_final: 0.7038 (p-90)
  outliers start: 16
  outliers final: 12
  residues processed: 126
  average time/residue: 0.2947
  time to fit residues: 49.5305
Evaluate side-chains
  124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 MET
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  519 GLU
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain C residue  545 MET
Chi-restraints excluded: chain D residue  345 THR
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  378 ARG
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  536 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0000
   chunk 64 optimal weight:    0.9980
   chunk 75 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 81 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7788

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

Flipped N/Q/H residues before XYZ refinement:
D 522 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.147094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.101364 restraints weight = 10303.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 1.56
r_work: 0.2854 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   9191  Z= 0.210
  Angle     :  0.536  10.453  12492  Z= 0.260
  Chirality :  0.039   0.155   1454
  Planarity :  0.004   0.045   1593
  Dihedral  :  4.507  50.793   1293
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.38 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.25), residues: 1153
  helix:  1.65 (0.20), residues: 693
  sheet: -1.67 (0.65), residues: 57
  loop : -0.83 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  81 
 HIS   0.003   0.001   HIS D 204 
 PHE   0.009   0.001   PHE C 181 
 TYR   0.019   0.001   TYR D  88 
 ARG   0.004   0.000   ARG C 452 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8308 (mmtt)
REVERT: C  451 ARG cc_start: 0.9037 (ttm110) cc_final: 0.8455 (mtm-85)
REVERT: C  549 GLN cc_start: 0.7740 (mp-120) cc_final: 0.7216 (mp10)
REVERT: D   15 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8490 (tp-100)
REVERT: D  329 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7399 (pt0)
REVERT: D  350 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8063 (mt)
REVERT: D  389 LYS cc_start: 0.8337 (mtmm) cc_final: 0.7712 (mtmm)
REVERT: D  427 TRP cc_start: 0.7353 (p-90) cc_final: 0.6988 (p-90)
  outliers start: 15
  outliers final: 12
  residues processed: 121
  average time/residue: 0.3636
  time to fit residues: 57.8119
Evaluate side-chains
  123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 1.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 MET
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain C residue  545 MET
Chi-restraints excluded: chain D residue  345 THR
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  459 LEU
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  536 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0010
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 108 optimal weight:    0.0770
   chunk 92 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.3744

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

Flipped N/Q/H residues before XYZ refinement:
C 225 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.147906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.102149 restraints weight = 10383.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.61
r_work: 0.2876 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.075   9191  Z= 0.163
  Angle     :  0.519  10.548  12492  Z= 0.251
  Chirality :  0.038   0.151   1454
  Planarity :  0.003   0.043   1593
  Dihedral  :  4.380  49.201   1293
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.81 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.25), residues: 1153
  helix:  1.87 (0.20), residues: 693
  sheet: -1.30 (0.70), residues: 50
  loop : -0.79 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D  81 
 HIS   0.003   0.001   HIS D 204 
 PHE   0.008   0.001   PHE C 181 
 TYR   0.020   0.001   TYR D  88 
 ARG   0.004   0.000   ARG C 452 

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

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

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2306 Ramachandran restraints generated.
    1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
REVERT: C   12 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8267 (mmtt)
REVERT: C   60 MET cc_start: 0.8575 (mmt) cc_final: 0.8133 (mmt)
REVERT: C  102 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8679 (mmmm)
REVERT: C  321 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7997 (mptt)
REVERT: C  444 GLU cc_start: 0.8502 (tt0) cc_final: 0.8155 (tm-30)
REVERT: C  448 GLU cc_start: 0.8484 (tp30) cc_final: 0.8210 (tp30)
REVERT: C  451 ARG cc_start: 0.9027 (ttm110) cc_final: 0.8573 (mtm110)
REVERT: C  452 ARG cc_start: 0.7887 (mtm110) cc_final: 0.7622 (ttm-80)
REVERT: C  549 GLN cc_start: 0.7696 (mp-120) cc_final: 0.7171 (mp10)
REVERT: D   15 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8491 (tp-100)
REVERT: D  329 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7374 (pt0)
REVERT: D  350 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8042 (mt)
REVERT: D  389 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7710 (mtmm)
REVERT: D  427 TRP cc_start: 0.7303 (p-90) cc_final: 0.6956 (p-90)
  outliers start: 12
  outliers final: 9
  residues processed: 127
  average time/residue: 0.2802
  time to fit residues: 47.6650
Evaluate side-chains
  124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 MET
Chi-restraints excluded: chain C residue   51 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  529 VAL
Chi-restraints excluded: chain D residue  345 THR
Chi-restraints excluded: chain D residue  350 ILE
Chi-restraints excluded: chain D residue  378 ARG
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  536 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 112 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 67 optimal weight:    0.2980
   chunk 98 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C 225 GLN
D 522 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.146785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.101059 restraints weight = 10449.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 1.57
r_work: 0.2849 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   9191  Z= 0.193
  Angle     :  0.535  12.271  12492  Z= 0.257
  Chirality :  0.039   0.213   1454
  Planarity :  0.004   0.046   1593
  Dihedral  :  4.364  49.915   1293
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 15.34 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.25), residues: 1153
  helix:  1.84 (0.20), residues: 693
  sheet: -1.53 (0.67), residues: 57
  loop : -0.76 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  81 
 HIS   0.003   0.001   HIS D 204 
 PHE   0.009   0.001   PHE C 291 
 TYR   0.019   0.001   TYR D  88 
 ARG   0.007   0.000   ARG C   2 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5098.96 seconds
wall clock time: 91 minutes 30.30 seconds (5490.30 seconds total)