Starting phenix.real_space_refine
on Thu Mar 13 18:23:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zdr_14667/03_2025/7zdr_14667_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zdr_14667/03_2025/7zdr_14667.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zdr_14667/03_2025/7zdr_14667.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zdr_14667/03_2025/7zdr_14667.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zdr_14667/03_2025/7zdr_14667_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zdr_14667/03_2025/7zdr_14667_neut.cif"
  }
  resolution = 3.05
  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=   0.006
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      29      5.16       5
     C    5770      2.51       5
     N    1584      2.21       5
     O    1627      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s

  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: 4415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4415
          Classifications: {'peptide': 573}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 18, 'TRANS': 554}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "D"
      Number of atoms: 4567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 585, 4567
          Classifications: {'peptide': 585}
          Link IDs: {'PTRANS': 27, 'TRANS': 557}
    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: 5.80, per 1000 atoms: 0.64
  Number of scatterers: 9014
  At special positions: 0
  Unit cell: (120.528, 77.841, 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      29     16.00
     P       3     15.00
     Mg      1     11.99
     O    1627      8.00
     N    1584      7.00
     C    5770      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: 2.30
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2142

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 6 sheets defined
      66.8% alpha, 6.5% 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: 3.844A  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: 3.523A  pdb=" N   ILE C  22 " --> pdb=" O   LEU C  18 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA C  25 " --> pdb=" O   GLY C  21 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE C  33 " --> pdb=" O   LEU C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 54
    Processing helix  chain 'C' and resid 59 through 104
      removed outlier: 3.579A  pdb=" N   TYR C  78 " --> pdb=" O   THR C  74 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE C  89 " --> pdb=" O   ALA C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 132
      removed outlier: 3.684A  pdb=" N   ASN C 121 " --> pdb=" O   GLY C 117 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA C 125 " --> pdb=" O   ASN C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 137
    Processing helix  chain 'C' and resid 137 through 156
    Processing helix  chain 'C' and resid 159 through 176
      removed outlier: 3.760A  pdb=" N   THR C 165 " --> pdb=" O   THR C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 185
    Processing helix  chain 'C' and resid 185 through 209
    Processing helix  chain 'C' and resid 209 through 216
      removed outlier: 3.510A  pdb=" N   ILE C 215 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 267
      removed outlier: 3.608A  pdb=" N   MET C 251 " --> pdb=" O   SER C 247 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET C 262 " --> pdb=" O   ALA C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 290
      removed outlier: 4.338A  pdb=" N   ALA C 281 " --> pdb=" O   GLY C 277 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU C 282 " --> pdb=" O   ALA C 278 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   PHE C 283 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 291 through 293
      No H-bonds generated for 'chain 'C' and resid 291 through 293'
    Processing helix  chain 'C' and resid 296 through 319
      removed outlier: 3.840A  pdb=" N   GLY C 305 " --> pdb=" O   PHE C 301 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLN C 306 " --> pdb=" O   GLN C 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 381 through 387
      removed outlier: 3.516A  pdb=" N   GLN C 385 " --> pdb=" O   THR C 381 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 407
      No H-bonds generated for 'chain 'C' and resid 405 through 407'
    Processing helix  chain 'C' and resid 408 through 415
      removed outlier: 3.741A  pdb=" N   GLN C 414 " --> pdb=" O   ALA C 410 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 442 through 454
      removed outlier: 3.532A  pdb=" N   SER C 447 " --> pdb=" O   ASP C 443 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 455 through 459
      removed outlier: 3.528A  pdb=" N   LEU C 458 " --> pdb=" O   LEU C 455 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 480 through 492
    Processing helix  chain 'C' and resid 506 through 520
      removed outlier: 3.686A  pdb=" N   GLN C 512 " --> pdb=" O   THR C 508 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 555 through 562
      removed outlier: 3.598A  pdb=" N   ARG C 562 " --> pdb=" O   GLU C 558 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 564 through 572
    Processing helix  chain 'D' and resid 5 through 16
    Processing helix  chain 'D' and resid 17 through 19
      No H-bonds generated for 'chain 'D' and resid 17 through 19'
    Processing helix  chain 'D' and resid 20 through 54
      removed outlier: 3.608A  pdb=" N   LEU D  24 " --> pdb=" O   SER D  20 " (cutoff:3.500A)
      removed outlier: 3.605A  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: 3.520A  pdb=" N   ILE D  94 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 115
    Processing helix  chain 'D' and resid 118 through 128
      removed outlier: 3.577A  pdb=" N   THR D 124 " --> pdb=" O   GLY D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 132
      No H-bonds generated for 'chain 'D' and resid 130 through 132'
    Processing helix  chain 'D' and resid 133 through 139
      removed outlier: 3.616A  pdb=" N   TYR D 137 " --> pdb=" O   MET D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 159
      removed outlier: 3.702A  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: 3.623A  pdb=" N   THR D 172 " --> pdb=" O   ILE D 168 " (cutoff:3.500A)
      removed outlier: 3.733A  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 187 through 194
      removed outlier: 3.656A  pdb=" N   ASN D 191 " --> pdb=" O   ALA D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 203
      removed outlier: 4.172A  pdb=" N   GLY D 203 " --> pdb=" O   ALA D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 203 through 211
    Processing helix  chain 'D' and resid 211 through 219
    Processing helix  chain 'D' and resid 220 through 273
      removed outlier: 4.085A  pdb=" N   GLU D 226 " --> pdb=" O   GLU D 222 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER D 227 " --> pdb=" O   ALA D 223 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLU D 241 " --> pdb=" O   GLN D 237 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   VAL D 242 " --> pdb=" O   ARG D 238 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU D 245 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LEU D 248 " --> pdb=" O   ARG D 244 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER D 249 " --> pdb=" O   LEU D 245 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER D 250 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU D 253 " --> pdb=" O   SER D 249 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU D 273 " --> pdb=" O   GLY D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 310
      removed outlier: 3.514A  pdb=" N   GLY D 290 " --> pdb=" O   THR D 286 " (cutoff:3.500A)
      Proline residue:  D 298  - end of helix
      removed outlier: 3.931A  pdb=" N   PHE D 301 " --> pdb=" O   ALA D 297 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
    Processing helix  chain 'D' and resid 310 through 330
      removed outlier: 3.558A  pdb=" N   LYS D 314 " --> pdb=" O   PHE D 310 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER D 323 " --> pdb=" O   GLY D 319 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   THR D 326 " --> pdb=" O   ASP D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 388 through 398
      removed outlier: 3.667A  pdb=" N   LEU D 392 " --> pdb=" O   GLY D 388 " (cutoff:3.500A)
      removed outlier: 3.849A  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
    Processing helix  chain 'D' and resid 473 through 477
      removed outlier: 4.015A  pdb=" N   ASP D 476 " --> pdb=" O   GLN D 473 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 487 through 500
    Processing helix  chain 'D' and resid 517 through 530
    Processing helix  chain 'D' and resid 566 through 572
      removed outlier: 3.792A  pdb=" N   VAL D 572 " --> pdb=" O   ALA D 568 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 575 through 587
      removed outlier: 3.502A  pdb=" N   ARG D 584 " --> pdb=" O   LEU D 580 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 359 through 362
      removed outlier: 7.388A  pdb=" N   LEU C 361 " --> pdb=" O   ARG C 342 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   ARG C 342 " --> pdb=" O   LEU C 361 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419
      removed outlier: 6.375A  pdb=" N   VAL C 496 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   VAL C 529 " --> pdb=" O   VAL C 496 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   LEU C 498 " --> pdb=" O   VAL C 529 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ILE C 369 " --> pdb=" O   MET C 528 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   THR C 530 " --> pdb=" O   ILE C 369 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   ILE C 371 " --> pdb=" O   THR C 530 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ALA C 370 " --> pdb=" O   ILE C 543 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   MET C 545 " --> pdb=" O   ALA C 370 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   LEU C 372 " --> pdb=" O   MET C 545 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   ILE C 542 " --> pdb=" O   GLN C 553 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLN C 553 " --> pdb=" O   ILE C 542 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   VAL C 544 " --> pdb=" O   ILE C 551 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 428 through 429
    Processing sheet with id=AA4, first strand: chain 'D' and resid 371 through 373
      removed outlier: 3.526A  pdb=" N   PHE D 371 " --> pdb=" O   ALA D 352 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 364 through 366
      removed outlier: 6.582A  pdb=" N   ILE D 357 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER D 401 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 425 through 429
      removed outlier: 7.115A  pdb=" N   SER D 426 " --> pdb=" O   LEU D 508 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   ASP D 510 " --> pdb=" O   SER D 426 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   VAL D 428 " --> pdb=" O   ASP D 510 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LEU D 507 " --> pdb=" O   LEU D 538 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   VAL D 540 " --> pdb=" O   LEU D 507 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   LEU D 509 " --> pdb=" O   VAL D 540 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   VAL D 380 " --> pdb=" O   TRP D 554 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   MET D 556 " --> pdb=" O   VAL D 380 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   VAL D 382 " --> pdb=" O   MET D 556 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ILE D 553 " --> pdb=" O   GLN D 564 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   GLN D 564 " --> pdb=" O   ILE D 553 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   VAL D 555 " --> pdb=" O   ILE D 562 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN D 557 " --> pdb=" O   ARG D 560 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ARG D 560 " --> pdb=" O   GLN D 557 " (cutoff:3.500A)

    536 hydrogen bonds defined for protein.
    1569 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: 4.05

  Time building geometry restraints manager: 2.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2897
        1.33 -     1.45: 1107
        1.45 -     1.57: 5127
        1.57 -     1.69: 5
        1.69 -     1.81: 56
  Bond restraints: 9192
  Sorted by residual:
  bond pdb=" O3A ANP D 602 "
       pdb=" PB  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.700  1.555  0.145 2.00e-02 2.50e+03 5.23e+01
  bond pdb=" N3B ANP D 602 "
       pdb=" PG  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.795  1.691  0.104 2.00e-02 2.50e+03 2.71e+01
  bond pdb=" O5' ANP D 602 "
       pdb=" PA  ANP D 602 "
    ideal  model  delta    sigma   weight residual
    1.655  1.580  0.075 2.00e-02 2.50e+03 1.42e+01
  bond pdb=" N   GLN D 377 "
       pdb=" CA  GLN D 377 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.23e-02 6.61e+03 7.10e+00
  bond pdb=" N   GLU C 350 "
       pdb=" CA  GLU C 350 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 1.31e-02 5.83e+03 6.88e+00
  ... (remaining 9187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.45: 12423
        3.45 -     6.89: 66
        6.89 -    10.34: 5
       10.34 -    13.78: 1
       13.78 -    17.23: 1
  Bond angle restraints: 12496
  Sorted by residual:
  angle pdb=" PB  ANP D 602 "
        pdb=" N3B ANP D 602 "
        pdb=" PG  ANP D 602 "
      ideal   model   delta    sigma   weight residual
     126.95  109.72   17.23 3.00e+00 1.11e-01 3.30e+01
  angle pdb=" N   ASN C 121 "
        pdb=" CA  ASN C 121 "
        pdb=" C   ASN C 121 "
      ideal   model   delta    sigma   weight residual
     112.89  108.02    4.87 1.24e+00 6.50e-01 1.54e+01
  angle pdb=" O1B ANP D 602 "
        pdb=" PB  ANP D 602 "
        pdb=" O2B ANP D 602 "
      ideal   model   delta    sigma   weight residual
     120.08  109.62   10.46 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" N   GLN C 248 "
        pdb=" CA  GLN C 248 "
        pdb=" C   GLN C 248 "
      ideal   model   delta    sigma   weight residual
     113.41  109.30    4.11 1.22e+00 6.72e-01 1.14e+01
  angle pdb=" CA  GLU C 350 "
        pdb=" C   GLU C 350 "
        pdb=" O   GLU C 350 "
      ideal   model   delta    sigma   weight residual
     121.81  118.07    3.74 1.18e+00 7.18e-01 1.01e+01
  ... (remaining 12491 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.64: 4989
       19.64 -    39.29: 433
       39.29 -    58.93: 51
       58.93 -    78.58: 24
       78.58 -    98.22: 5
  Dihedral angle restraints: 5502
    sinusoidal: 2180
      harmonic: 3322
  Sorted by residual:
  dihedral pdb=" CA  LYS C  12 "
           pdb=" C   LYS C  12 "
           pdb=" N   ARG C  13 "
           pdb=" CA  ARG C  13 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.03   17.97     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  MET D 556 "
           pdb=" C   MET D 556 "
           pdb=" N   GLN D 557 "
           pdb=" CA  GLN D 557 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.43   17.57     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" O1B ANP D 602 "
           pdb=" N3B ANP D 602 "
           pdb=" PB  ANP D 602 "
           pdb=" PG  ANP D 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15  -63.07   98.22     1      3.00e+01 1.11e-03 1.22e+01
  ... (remaining 5499 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1177
       0.054 -    0.108: 247
       0.108 -    0.162: 26
       0.162 -    0.215: 3
       0.215 -    0.269: 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   -2.63    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  TYR C 348 "
            pdb=" N   TYR C 348 "
            pdb=" C   TYR C 348 "
            pdb=" CB  TYR C 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  GLN C 232 "
            pdb=" N   GLN C 232 "
            pdb=" C   GLN C 232 "
            pdb=" CB  GLN C 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.61e-01
  ... (remaining 1451 not shown)

  Planarity restraints: 1595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 347 "    0.016 2.00e-02 2.50e+03   3.16e-02 9.96e+00
        pdb=" C   THR C 347 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   THR C 347 "    0.020 2.00e-02 2.50e+03
        pdb=" N   TYR C 348 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 178 "    0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO C 179 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO C 179 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 179 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 552 "   -0.007 2.00e-02 2.50e+03   1.35e-02 1.82e+00
        pdb=" C   GLU C 552 "    0.023 2.00e-02 2.50e+03
        pdb=" O   GLU C 552 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLN C 553 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1592 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 61
        2.61 -     3.18: 7681
        3.18 -     3.75: 13885
        3.75 -     4.33: 19631
        4.33 -     4.90: 32804
  Nonbonded interactions: 74062
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 390 "
            pdb="MG    MG D 601 "
     model   vdw
     2.031 2.170
  nonbonded pdb="MG    MG D 601 "
            pdb=" O1G ANP D 602 "
     model   vdw
     2.056 2.170
  nonbonded pdb=" OE1 GLN D 129 "
            pdb=" OG  SER D 323 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" NH2 ARG D   5 "
            pdb=" OD1 ASP D 322 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OG  SER C 438 "
            pdb=" OG  SER C 441 "
     model   vdw
     2.213 3.040
  ... (remaining 74057 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:             2.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.440
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
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      :  0.006   0.145   9192  Z= 0.396
  Angle     :  0.708  17.228  12496  Z= 0.378
  Chirality :  0.044   0.269   1454
  Planarity :  0.004   0.039   1595
  Dihedral  : 15.073  98.223   3360
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.22), residues: 1154
  helix: -1.59 (0.18), residues: 687
  sheet:  0.34 (0.70), residues: 52
  loop : -1.17 (0.26), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 427 
 HIS   0.005   0.001   HIS C 368 
 PHE   0.010   0.001   PHE D  73 
 TYR   0.015   0.001   TYR D 311 
 ARG   0.020   0.001   ARG D 560 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 1.049 
Fit side-chains
REVERT: C  343 ASP cc_start: 0.7857 (t0) cc_final: 0.7495 (t0)
REVERT: C  541 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7819 (tp40)
REVERT: D  311 TYR cc_start: 0.7620 (t80) cc_final: 0.7407 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.2612
  time to fit residues: 38.1971
Evaluate side-chains
  92 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0980
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 90 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
C 225 GLN
C 248 GLN
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 424 HIS
C 553 GLN
C 563 GLN
D  15 GLN
D 394 ASN
D 433 GLN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 461 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.138475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.103469 restraints weight = 10537.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.76
r_work: 0.2975 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9192  Z= 0.240
  Angle     :  0.619   8.073  12496  Z= 0.315
  Chirality :  0.041   0.157   1454
  Planarity :  0.005   0.040   1595
  Dihedral  :  7.508  88.756   1294
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  6.95 %
    Favored  : 92.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.23), residues: 1154
  helix:  0.11 (0.19), residues: 717
  sheet:  0.18 (0.73), residues: 47
  loop : -1.12 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  81 
 HIS   0.006   0.001   HIS C 368 
 PHE   0.014   0.001   PHE C 346 
 TYR   0.019   0.002   TYR D  88 
 ARG   0.008   0.001   ARG D 139 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 1.021 
Fit side-chains
REVERT: C  343 ASP cc_start: 0.8288 (t0) cc_final: 0.7835 (t0)
REVERT: C  506 ASP cc_start: 0.7460 (p0) cc_final: 0.6805 (t0)
REVERT: C  541 GLN cc_start: 0.8260 (tp-100) cc_final: 0.7848 (tp-100)
REVERT: D   94 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8911 (mp)
REVERT: D  154 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8161 (mp)
REVERT: D  311 TYR cc_start: 0.7908 (t80) cc_final: 0.7651 (t80)
REVERT: D  563 GLU cc_start: 0.8392 (tt0) cc_final: 0.8182 (mt-10)
REVERT: D  587 GLU cc_start: 0.7424 (tt0) cc_final: 0.7219 (tt0)
  outliers start: 7
  outliers final: 3
  residues processed: 112
  average time/residue: 0.2657
  time to fit residues: 39.5447
Evaluate side-chains
  99 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 16 optimal weight:    0.2980
   chunk 77 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 237 GLN
C 394 GLN
C 549 GLN
D 143 GLN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.140171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.105566 restraints weight = 10599.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.71
r_work: 0.3006 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9192  Z= 0.200
  Angle     :  0.543   7.973  12496  Z= 0.274
  Chirality :  0.040   0.137   1454
  Planarity :  0.004   0.038   1595
  Dihedral  :  6.228  88.496   1294
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.23 %
    Favored  : 87.70 %
  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:  0.39 (0.24), residues: 1154
  helix:  0.97 (0.19), residues: 715
  sheet:  0.36 (0.74), residues: 47
  loop : -1.00 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  81 
 HIS   0.005   0.001   HIS C 368 
 PHE   0.016   0.001   PHE C 346 
 TYR   0.020   0.002   TYR D  88 
 ARG   0.010   0.000   ARG D 139 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 1.010 
Fit side-chains
REVERT: C  118 GLU cc_start: 0.7478 (pt0) cc_final: 0.7230 (pp20)
REVERT: C  343 ASP cc_start: 0.8348 (t0) cc_final: 0.7846 (t0)
REVERT: C  448 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8440 (tm-30)
REVERT: D   94 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8944 (mp)
REVERT: D  154 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8421 (mt)
REVERT: D  234 ASP cc_start: 0.8327 (t0) cc_final: 0.8096 (t0)
REVERT: D  311 TYR cc_start: 0.7905 (t80) cc_final: 0.7689 (t80)
  outliers start: 10
  outliers final: 6
  residues processed: 111
  average time/residue: 0.2419
  time to fit residues: 36.7570
Evaluate side-chains
  102 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  167 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0050
   chunk 27 optimal weight:    0.0870
   chunk 71 optimal weight:    0.1980
   chunk 35 optimal weight:    8.9990
   chunk 108 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.6576

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

Flipped N/Q/H residues before XYZ refinement:
C 225 GLN
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.141226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.106658 restraints weight = 10432.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.69
r_work: 0.2996 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9192  Z= 0.187
  Angle     :  0.518   7.756  12496  Z= 0.262
  Chirality :  0.039   0.136   1454
  Planarity :  0.004   0.044   1595
  Dihedral  :  5.793  86.608   1294
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.51 %
    Favored  : 85.67 %
  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:  0.85 (0.24), residues: 1154
  helix:  1.40 (0.20), residues: 715
  sheet:  0.35 (0.75), residues: 47
  loop : -0.94 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  81 
 HIS   0.004   0.001   HIS C 368 
 PHE   0.017   0.001   PHE C 346 
 TYR   0.020   0.001   TYR D  88 
 ARG   0.009   0.000   ARG D 139 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 1.036 
Fit side-chains
REVERT: C  118 GLU cc_start: 0.7422 (pt0) cc_final: 0.7177 (pp20)
REVERT: C  343 ASP cc_start: 0.8281 (t0) cc_final: 0.7707 (t0)
REVERT: C  506 ASP cc_start: 0.7219 (p0) cc_final: 0.6439 (t0)
REVERT: D   94 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8946 (mp)
REVERT: D  154 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8442 (mt)
REVERT: D  234 ASP cc_start: 0.8281 (t0) cc_final: 0.8014 (t0)
REVERT: D  311 TYR cc_start: 0.7819 (t80) cc_final: 0.7589 (t80)
REVERT: D  460 ASP cc_start: 0.8245 (m-30) cc_final: 0.8017 (m-30)
REVERT: D  529 ASN cc_start: 0.8322 (t0) cc_final: 0.8025 (m-40)
  outliers start: 17
  outliers final: 10
  residues processed: 116
  average time/residue: 0.2461
  time to fit residues: 39.0021
Evaluate side-chains
  109 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  167 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 70 optimal weight:    0.2980
   chunk 87 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   chunk 105 optimal weight:    8.9990
   chunk 41 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 421 GLN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 557 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.141769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.107192 restraints weight = 10521.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 1.71
r_work: 0.3002 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9192  Z= 0.183
  Angle     :  0.505   6.769  12496  Z= 0.256
  Chirality :  0.039   0.252   1454
  Planarity :  0.004   0.047   1595
  Dihedral  :  5.620  83.706   1294
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.26 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.25), residues: 1154
  helix:  1.60 (0.20), residues: 713
  sheet:  0.33 (0.77), residues: 47
  loop : -0.90 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  81 
 HIS   0.004   0.001   HIS C 368 
 PHE   0.019   0.001   PHE C 346 
 TYR   0.015   0.001   TYR D  88 
 ARG   0.009   0.000   ARG D 139 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.936 
Fit side-chains
REVERT: C  118 GLU cc_start: 0.7506 (pt0) cc_final: 0.7252 (pp20)
REVERT: C  343 ASP cc_start: 0.8325 (t0) cc_final: 0.7752 (t0)
REVERT: C  541 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7579 (tp-100)
REVERT: D   94 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8948 (mp)
REVERT: D  154 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8510 (mt)
REVERT: D  234 ASP cc_start: 0.8318 (t0) cc_final: 0.8077 (t0)
REVERT: D  311 TYR cc_start: 0.7924 (t80) cc_final: 0.7704 (t80)
REVERT: D  460 ASP cc_start: 0.8145 (m-30) cc_final: 0.7932 (m-30)
REVERT: D  529 ASN cc_start: 0.8339 (t0) cc_final: 0.8070 (m-40)
  outliers start: 16
  outliers final: 9
  residues processed: 112
  average time/residue: 0.2600
  time to fit residues: 41.1396
Evaluate side-chains
  109 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  167 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 112 optimal weight:    0.3980
   chunk 95 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
C 225 GLN
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 549 GLN
** D 442 ASN ** 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 = 0.3607 r_free = 0.3607 target = 0.139469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.104627 restraints weight = 10455.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 1.69
r_work: 0.2989 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9192  Z= 0.268
  Angle     :  0.559   8.951  12496  Z= 0.279
  Chirality :  0.042   0.244   1454
  Planarity :  0.004   0.041   1595
  Dihedral  :  5.660  80.786   1294
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.69 %
    Favored  : 84.60 %
  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:  0.92 (0.25), residues: 1154
  helix:  1.46 (0.19), residues: 715
  sheet:  0.25 (0.77), residues: 47
  loop : -0.91 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  81 
 HIS   0.004   0.001   HIS C 368 
 PHE   0.020   0.001   PHE C 346 
 TYR   0.018   0.002   TYR D  88 
 ARG   0.010   0.000   ARG D 560 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.904 
Fit side-chains
REVERT: C  118 GLU cc_start: 0.7529 (pt0) cc_final: 0.7322 (pp20)
REVERT: C  343 ASP cc_start: 0.8402 (t0) cc_final: 0.7814 (t0)
REVERT: C  506 ASP cc_start: 0.7223 (p0) cc_final: 0.6476 (t0)
REVERT: C  541 GLN cc_start: 0.8120 (tp-100) cc_final: 0.7564 (tp-100)
REVERT: D   94 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.8991 (mp)
REVERT: D  154 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8544 (mt)
REVERT: D  234 ASP cc_start: 0.8334 (t0) cc_final: 0.8087 (t0)
REVERT: D  311 TYR cc_start: 0.7928 (t80) cc_final: 0.7723 (t80)
REVERT: D  460 ASP cc_start: 0.8137 (m-30) cc_final: 0.7916 (m-30)
REVERT: D  529 ASN cc_start: 0.8407 (t0) cc_final: 0.8115 (m-40)
  outliers start: 16
  outliers final: 11
  residues processed: 111
  average time/residue: 0.2368
  time to fit residues: 36.2359
Evaluate side-chains
  112 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  185 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 85 optimal weight:    0.2980
   chunk 14 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 70 optimal weight:    0.1980
   chunk 69 optimal weight:    1.9990
   chunk 111 optimal weight:    0.3980
   chunk 107 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
C 225 GLN
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 400 ASN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 557 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 = 0.142131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.106901 restraints weight = 10610.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.78
r_work: 0.3019 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9192  Z= 0.169
  Angle     :  0.506   7.602  12496  Z= 0.256
  Chirality :  0.039   0.193   1454
  Planarity :  0.004   0.046   1595
  Dihedral  :  5.497  80.250   1294
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.65 %
    Favored  : 83.64 %
  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: 1154
  helix:  1.72 (0.20), residues: 716
  sheet:  0.17 (0.78), residues: 47
  loop : -0.86 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C 368 
 PHE   0.021   0.001   PHE C 346 
 TYR   0.017   0.001   TYR D  88 
 ARG   0.011   0.000   ARG D 560 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 1.043 
Fit side-chains
REVERT: C  343 ASP cc_start: 0.8394 (t0) cc_final: 0.7803 (t0)
REVERT: C  506 ASP cc_start: 0.7251 (p0) cc_final: 0.6423 (t0)
REVERT: C  541 GLN cc_start: 0.8019 (tp-100) cc_final: 0.7472 (tp-100)
REVERT: D   94 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.8961 (mp)
REVERT: D  154 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8529 (mt)
REVERT: D  234 ASP cc_start: 0.8328 (t0) cc_final: 0.8086 (t0)
REVERT: D  311 TYR cc_start: 0.7926 (t80) cc_final: 0.7702 (t80)
REVERT: D  342 LEU cc_start: 0.8915 (tp) cc_final: 0.8689 (tp)
REVERT: D  460 ASP cc_start: 0.8096 (m-30) cc_final: 0.7893 (m-30)
REVERT: D  529 ASN cc_start: 0.8336 (t0) cc_final: 0.8092 (m-40)
  outliers start: 16
  outliers final: 11
  residues processed: 112
  average time/residue: 0.2382
  time to fit residues: 36.7063
Evaluate side-chains
  112 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  400 ASN
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  185 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 100 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0980
   chunk 41 optimal weight:    0.0370
   chunk 38 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 98 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.3858

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

Flipped N/Q/H residues before XYZ refinement:
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 400 ASN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.140378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.105241 restraints weight = 10695.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.77
r_work: 0.3033 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9192  Z= 0.156
  Angle     :  0.503   7.265  12496  Z= 0.253
  Chirality :  0.039   0.176   1454
  Planarity :  0.004   0.051   1595
  Dihedral  :  5.388  78.624   1294
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.76 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.25), residues: 1154
  helix:  1.87 (0.20), residues: 711
  sheet:  0.17 (0.79), residues: 47
  loop : -0.87 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  81 
 HIS   0.003   0.000   HIS C 368 
 PHE   0.021   0.001   PHE C 346 
 TYR   0.017   0.001   TYR D  88 
 ARG   0.012   0.000   ARG D 560 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 1.042 
Fit side-chains
REVERT: C  343 ASP cc_start: 0.8377 (t0) cc_final: 0.7608 (t0)
REVERT: C  506 ASP cc_start: 0.7203 (p0) cc_final: 0.6368 (t0)
REVERT: C  541 GLN cc_start: 0.8003 (tp-100) cc_final: 0.7434 (tp-100)
REVERT: D   94 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8940 (mp)
REVERT: D  234 ASP cc_start: 0.8300 (t0) cc_final: 0.8065 (t0)
REVERT: D  311 TYR cc_start: 0.7900 (t80) cc_final: 0.7676 (t80)
REVERT: D  342 LEU cc_start: 0.8862 (tp) cc_final: 0.8626 (tp)
REVERT: D  463 TRP cc_start: 0.8894 (m100) cc_final: 0.8674 (m100)
REVERT: D  529 ASN cc_start: 0.8306 (t0) cc_final: 0.8104 (m-40)
REVERT: D  566 ARG cc_start: 0.7503 (mtp85) cc_final: 0.7080 (mtt180)
  outliers start: 17
  outliers final: 12
  residues processed: 112
  average time/residue: 0.2596
  time to fit residues: 39.8153
Evaluate side-chains
  111 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  133 MET
Chi-restraints excluded: chain D residue  185 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 456 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.141278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.106519 restraints weight = 10644.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.70
r_work: 0.3038 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9192  Z= 0.204
  Angle     :  0.519   7.922  12496  Z= 0.260
  Chirality :  0.040   0.203   1454
  Planarity :  0.004   0.054   1595
  Dihedral  :  5.387  76.686   1294
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.19 %
    Favored  : 83.32 %
  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:  1.26 (0.25), residues: 1154
  helix:  1.80 (0.20), residues: 710
  sheet:  0.13 (0.79), residues: 47
  loop : -0.85 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  81 
 HIS   0.003   0.001   HIS C 368 
 PHE   0.023   0.001   PHE C 346 
 TYR   0.018   0.001   TYR D  88 
 ARG   0.012   0.000   ARG D 560 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.790 
Fit side-chains
REVERT: C  343 ASP cc_start: 0.8344 (t0) cc_final: 0.7558 (t0)
REVERT: C  506 ASP cc_start: 0.7205 (p0) cc_final: 0.6379 (t0)
REVERT: C  541 GLN cc_start: 0.8043 (tp-100) cc_final: 0.7483 (tp-100)
REVERT: D   94 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8953 (mp)
REVERT: D  234 ASP cc_start: 0.8284 (t0) cc_final: 0.8043 (t0)
REVERT: D  311 TYR cc_start: 0.7887 (t80) cc_final: 0.7652 (t80)
REVERT: D  342 LEU cc_start: 0.8860 (tp) cc_final: 0.8591 (tp)
  outliers start: 14
  outliers final: 12
  residues processed: 108
  average time/residue: 0.3492
  time to fit residues: 51.9498
Evaluate side-chains
  110 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  185 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 108 optimal weight:    8.9990
   chunk 92 optimal weight:    0.9980
   chunk 89 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.141388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.105957 restraints weight = 10689.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.79
r_work: 0.3025 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9192  Z= 0.210
  Angle     :  0.533   9.580  12496  Z= 0.266
  Chirality :  0.040   0.203   1454
  Planarity :  0.004   0.056   1595
  Dihedral  :  5.367  75.565   1294
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.29 %
    Favored  : 83.21 %
  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:  1.25 (0.25), residues: 1154
  helix:  1.80 (0.20), residues: 709
  sheet:  0.08 (0.78), residues: 47
  loop : -0.85 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  81 
 HIS   0.004   0.001   HIS C 368 
 PHE   0.024   0.001   PHE C 346 
 TYR   0.019   0.001   TYR D  88 
 ARG   0.013   0.000   ARG D 560 

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

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

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2308 Ramachandran restraints generated.
    1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.946 
Fit side-chains
REVERT: C  343 ASP cc_start: 0.8339 (t0) cc_final: 0.7576 (t0)
REVERT: C  506 ASP cc_start: 0.7209 (p0) cc_final: 0.6406 (t0)
REVERT: C  541 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7457 (tp-100)
REVERT: D   94 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8956 (mp)
REVERT: D  234 ASP cc_start: 0.8325 (t0) cc_final: 0.8082 (t0)
REVERT: D  311 TYR cc_start: 0.7893 (t80) cc_final: 0.7672 (t80)
REVERT: D  342 LEU cc_start: 0.8818 (tp) cc_final: 0.8562 (tp)
  outliers start: 14
  outliers final: 12
  residues processed: 109
  average time/residue: 0.2524
  time to fit residues: 38.4880
Evaluate side-chains
  110 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  260 ILE
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  419 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  452 ARG
Chi-restraints excluded: chain C residue  530 THR
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  167 LEU
Chi-restraints excluded: chain D residue  185 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 112 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 86 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.141074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.105626 restraints weight = 10624.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 1.78
r_work: 0.3010 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9192  Z= 0.213
  Angle     :  0.539  10.517  12496  Z= 0.267
  Chirality :  0.040   0.204   1454
  Planarity :  0.004   0.056   1595
  Dihedral  :  5.353  74.371   1294
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 15.19 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.25), residues: 1154
  helix:  1.77 (0.20), residues: 710
  sheet:  0.07 (0.79), residues: 47
  loop : -0.85 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  81 
 HIS   0.004   0.001   HIS C 368 
 PHE   0.025   0.001   PHE C 346 
 TYR   0.019   0.001   TYR D  88 
 ARG   0.013   0.000   ARG D 560 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4794.54 seconds
wall clock time: 85 minutes 15.25 seconds (5115.25 seconds total)