Starting phenix.real_space_refine
on Wed Feb 12 17:32:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wpc_32682/02_2025/7wpc_32682_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wpc_32682/02_2025/7wpc_32682.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wpc_32682/02_2025/7wpc_32682.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wpc_32682/02_2025/7wpc_32682.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wpc_32682/02_2025/7wpc_32682_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wpc_32682/02_2025/7wpc_32682_neut.cif"
  }
  resolution = 2.57
  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=   0.012
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
     Zn      1      6.06       5
     S      44      5.16       5
     Cl      1      4.86       5
     C    5162      2.51       5
     N    1335      2.21       5
     O    1514      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8057
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1582
          Classifications: {'peptide': 197}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 183}
    Chain: "B"
      Number of atoms: 1518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1518
          Classifications: {'peptide': 188}
          Link IDs: {'PTRANS': 10, 'TRANS': 177}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 4857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4857
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 27, 'TRANS': 567}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 44
          Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 6.37, per 1000 atoms: 0.79
  Number of scatterers: 8057
  At special positions: 0
  Unit cell: (99.704, 98.056, 127.72, 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)
     Zn      1     29.99
     Cl      1     17.00
     S      44     16.00
     O    1514      8.00
     N    1335      7.00
     C    5162      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 388 " - pdb=" SG  CYS A 522 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 477 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 333 " - pdb=" SG  CYS B 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 376 " - pdb=" SG  CYS B 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 477 " - pdb=" SG  CYS B 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 340 "
      " NAG D 903 " - " ASN D  90 "
      " NAG D 904 " - " ASN D 322 "
      " NAG D 905 " - " ASN D 546 "
      " NAG E   1 " - " ASN B 340 "
  Time building additional restraints: 2.01
  Conformation dependent library (CDL) restraints added in 844.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D 902 "
        pdb="ZN    ZN D 902 " - pdb=" NE2 HIS D 374 "


  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1848

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 8 sheets defined
      44.5% alpha, 7.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 334 through 340
      removed outlier: 3.958A  pdb=" N   VAL A 338 " --> pdb=" O   PRO A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 368
      removed outlier: 3.992A  pdb=" N   ASN A 367 " --> pdb=" O   VAL A 364 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LEU A 368 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 364 through 368'
    Processing helix  chain 'A' and resid 402 through 404
      No H-bonds generated for 'chain 'A' and resid 402 through 404'
    Processing helix  chain 'A' and resid 414 through 419
    Processing helix  chain 'B' and resid 335 through 340
    Processing helix  chain 'B' and resid 363 through 368
      removed outlier: 3.972A  pdb=" N   TYR B 366 " --> pdb=" O   SER B 363 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   LEU B 368 " --> pdb=" O   LEU B 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 387
      removed outlier: 3.557A  pdb=" N   ASP B 386 " --> pdb=" O   LYS B 383 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   LEU B 387 " --> pdb=" O   LEU B 384 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 383 through 387'
    Processing helix  chain 'B' and resid 402 through 404
      No H-bonds generated for 'chain 'B' and resid 402 through 404'
    Processing helix  chain 'B' and resid 414 through 419
    Processing helix  chain 'D' and resid 20 through 53
      removed outlier: 3.509A  pdb=" N   GLN D  24 " --> pdb=" O   THR D  20 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   GLU D  37 " --> pdb=" O   ASN D  33 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASP D  38 " --> pdb=" O   HIS D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 56 through 80
      removed outlier: 3.809A  pdb=" N   GLN D  60 " --> pdb=" O   GLU D  56 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASN D  61 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASP D  67 " --> pdb=" O   ASN D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 81 through 83
      No H-bonds generated for 'chain 'D' and resid 81 through 83'
    Processing helix  chain 'D' and resid 90 through 101
    Processing helix  chain 'D' and resid 103 through 108
      removed outlier: 4.047A  pdb=" N   VAL D 107 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU D 108 " --> pdb=" O   SER D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 130
      removed outlier: 3.590A  pdb=" N   ARG D 115 " --> pdb=" O   ASP D 111 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ASN D 117 " --> pdb=" O   SER D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 147 through 155
      removed outlier: 3.611A  pdb=" N   ALA D 153 " --> pdb=" O   ASN D 149 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ASN D 154 " --> pdb=" O   GLU D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 172
      removed outlier: 3.718A  pdb=" N   ARG D 161 " --> pdb=" O   ASP D 157 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TRP D 168 " --> pdb=" O   ALA D 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 173 through 175
      No H-bonds generated for 'chain 'D' and resid 173 through 175'
    Processing helix  chain 'D' and resid 176 through 194
      removed outlier: 3.558A  pdb=" N   GLU D 182 " --> pdb=" O   PRO D 178 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   VAL D 185 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 204
      removed outlier: 3.503A  pdb=" N   TYR D 202 " --> pdb=" O   ASP D 198 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 205 through 208
    Processing helix  chain 'D' and resid 219 through 221
      No H-bonds generated for 'chain 'D' and resid 219 through 221'
    Processing helix  chain 'D' and resid 222 through 227
    Processing helix  chain 'D' and resid 233 through 249
      removed outlier: 3.646A  pdb=" N   HIS D 239 " --> pdb=" O   PRO D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 265 through 267
      No H-bonds generated for 'chain 'D' and resid 265 through 267'
    Processing helix  chain 'D' and resid 275 through 279
      removed outlier: 3.929A  pdb=" N   TYR D 279 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 293 through 298
    Processing helix  chain 'D' and resid 303 through 316
    Processing helix  chain 'D' and resid 324 through 330
      removed outlier: 3.640A  pdb=" N   TRP D 328 " --> pdb=" O   THR D 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 383
      removed outlier: 3.604A  pdb=" N   HIS D 373 " --> pdb=" O   PHE D 369 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   HIS D 378 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 399 through 413
      removed outlier: 3.795A  pdb=" N   ALA D 403 " --> pdb=" O   GLY D 399 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLY D 405 " --> pdb=" O   HIS D 401 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   SER D 411 " --> pdb=" O   ILE D 407 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 447
      removed outlier: 3.728A  pdb=" N   GLU D 435 " --> pdb=" O   ASP D 431 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ASN D 437 " --> pdb=" O   GLU D 433 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   THR D 445 " --> pdb=" O   LYS D 441 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 449 through 465
    Processing helix  chain 'D' and resid 472 through 484
      removed outlier: 3.536A  pdb=" N   LYS D 476 " --> pdb=" O   GLN D 472 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLU D 479 " --> pdb=" O   LYS D 475 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ARG D 482 " --> pdb=" O   TRP D 478 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 499 through 502
      removed outlier: 3.501A  pdb=" N   SER D 502 " --> pdb=" O   ASP D 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 499 through 502'
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
      removed outlier: 3.648A  pdb=" N   LEU D 520 " --> pdb=" O   TYR D 516 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE D 523 " --> pdb=" O   THR D 519 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 542
      removed outlier: 3.594A  pdb=" N   LYS D 541 " --> pdb=" O   PRO D 538 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   CYS D 542 " --> pdb=" O   LEU D 539 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 538 through 542'
    Processing helix  chain 'D' and resid 550 through 559
      removed outlier: 3.809A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 572
      removed outlier: 3.884A  pdb=" N   GLU D 571 " --> pdb=" O   THR D 567 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 581 through 588
      removed outlier: 3.506A  pdb=" N   TYR D 587 " --> pdb=" O   PRO D 583 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE D 588 " --> pdb=" O   LEU D 584 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355
      removed outlier: 3.693A  pdb=" N   ASN A 351 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER A 396 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LYS A 375 " --> pdb=" O   VAL A 430 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 449 through 451
    Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 471
      removed outlier: 3.579A  pdb=" N   TYR A 486 " --> pdb=" O   TYR A 470 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 353 through 355
      removed outlier: 4.169A  pdb=" N   LYS B 375 " --> pdb=" O   VAL B 430 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 449 through 451
    Processing sheet with id=AA6, first strand: chain 'D' and resid 132 through 133
    Processing sheet with id=AA7, first strand: chain 'D' and resid 262 through 263
      removed outlier: 5.772A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'D' and resid 347 through 352
      removed outlier: 3.661A  pdb=" N   ARG D 357 " --> pdb=" O   TRP D 349 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   ASP D 355 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)

    280 hydrogen bonds defined for protein.
    795 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: 2.04

  Time building geometry restraints manager: 2.29 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2559
        1.35 -     1.47: 2162
        1.47 -     1.59: 3493
        1.59 -     1.71: 0
        1.71 -     1.83: 65
  Bond restraints: 8279
  Sorted by residual:
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.470 -0.064 2.00e-02 2.50e+03 1.03e+01
  bond pdb=" N   VAL B 480 "
       pdb=" CA  VAL B 480 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.31e+00
  bond pdb=" N   TYR B 486 "
       pdb=" CA  TYR B 486 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.19e-02 7.06e+03 7.59e+00
  bond pdb=" N   LEU B 514 "
       pdb=" CA  LEU B 514 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.029 1.23e-02 6.61e+03 5.54e+00
  bond pdb=" N   CYS B 485 "
       pdb=" CA  CYS B 485 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.29e-02 6.01e+03 5.38e+00
  ... (remaining 8274 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 10925
        1.89 -     3.78: 267
        3.78 -     5.68: 39
        5.68 -     7.57: 12
        7.57 -     9.46: 4
  Bond angle restraints: 11247
  Sorted by residual:
  angle pdb=" N   VAL D 339 "
        pdb=" CA  VAL D 339 "
        pdb=" C   VAL D 339 "
      ideal   model   delta    sigma   weight residual
     113.71  108.44    5.27 9.50e-01 1.11e+00 3.07e+01
  angle pdb=" CA  GLY B 482 "
        pdb=" C   GLY B 482 "
        pdb=" O   GLY B 482 "
      ideal   model   delta    sigma   weight residual
     122.01  118.07    3.94 9.70e-01 1.06e+00 1.65e+01
  angle pdb=" N   GLY A 499 "
        pdb=" CA  GLY A 499 "
        pdb=" C   GLY A 499 "
      ideal   model   delta    sigma   weight residual
     111.34  118.64   -7.30 1.82e+00 3.02e-01 1.61e+01
  angle pdb=" N   GLU D 145 "
        pdb=" CA  GLU D 145 "
        pdb=" C   GLU D 145 "
      ideal   model   delta    sigma   weight residual
     109.81  118.47   -8.66 2.21e+00 2.05e-01 1.54e+01
  angle pdb=" CA  PHE B 512 "
        pdb=" CB  PHE B 512 "
        pdb=" CG  PHE B 512 "
      ideal   model   delta    sigma   weight residual
     113.80  117.43   -3.63 1.00e+00 1.00e+00 1.32e+01
  ... (remaining 11242 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.38: 4594
       22.38 -    44.76: 320
       44.76 -    67.15: 35
       67.15 -    89.53: 7
       89.53 -   111.91: 25
  Dihedral angle restraints: 4981
    sinusoidal: 2101
      harmonic: 2880
  Sorted by residual:
  dihedral pdb=" CA  PHE A 372 "
           pdb=" C   PHE A 372 "
           pdb=" N   THR A 373 "
           pdb=" CA  THR A 373 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.39   20.61     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" C3  NAG E   1 "
           pdb=" C1  NAG E   1 "
           pdb=" C2  NAG E   1 "
           pdb=" O5  NAG E   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -55.55   56.36 -111.91     1      3.00e+01 1.11e-03 1.46e+01
  dihedral pdb=" N2  NAG E   1 "
           pdb=" C1  NAG E   1 "
           pdb=" C2  NAG E   1 "
           pdb=" O5  NAG E   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.19  -66.52 -111.67     1      3.00e+01 1.11e-03 1.46e+01
  ... (remaining 4978 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1033
       0.064 -    0.129: 152
       0.129 -    0.193: 6
       0.193 -    0.258: 4
       0.258 -    0.322: 2
  Chirality restraints: 1197
  Sorted by residual:
  chirality pdb=" CA  LEU B 515 "
            pdb=" N   LEU B 515 "
            pdb=" C   LEU B 515 "
            pdb=" CB  LEU B 515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.43    0.03 2.00e-02 2.50e+03 2.35e+00
  chirality pdb=" CA  ASN B 484 "
            pdb=" N   ASN B 484 "
            pdb=" C   ASN B 484 "
            pdb=" CB  ASN B 484 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.78e+00
  ... (remaining 1194 not shown)

  Planarity restraints: 1453
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 564 "    0.042 5.00e-02 4.00e+02   6.34e-02 6.44e+00
        pdb=" N   PRO D 565 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO D 565 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 565 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 499 "   -0.040 5.00e-02 4.00e+02   5.98e-02 5.73e+00
        pdb=" N   PRO D 500 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO D 500 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D 500 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 582 "   -0.037 5.00e-02 4.00e+02   5.51e-02 4.86e+00
        pdb=" N   PRO D 583 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO D 583 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D 583 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1450 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1689
        2.78 -     3.31: 6569
        3.31 -     3.84: 13351
        3.84 -     4.37: 15369
        4.37 -     4.90: 26616
  Nonbonded interactions: 63594
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D 402 "
            pdb="ZN    ZN D 902 "
     model   vdw
     2.253 2.230
  nonbonded pdb=" O   THR D 118 "
            pdb=" OG1 THR D 122 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OG1 THR B 412 "
            pdb=" OD2 ASP B 417 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OG  SER D 109 "
            pdb=" OD1 ASP D 111 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" OG  SER B 466 "
            pdb=" OE1 GLU B 468 "
     model   vdw
     2.354 3.040
  ... (remaining 63589 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 329 through 369 or resid 372 through 499 or resid 501 thro \ 
ugh 515 or resid 523 through 525))
  selection = (chain 'B' and resid 329 through 525)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}

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:             11.450
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     22.920
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8279  Z= 0.237
  Angle     :  0.720   9.460  11247  Z= 0.420
  Chirality :  0.048   0.322   1197
  Planarity :  0.006   0.063   1448
  Dihedral  : 17.016 111.911   3103
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.52 %
    Favored  : 95.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.11 %
    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: -4.19 (0.20), residues: 968
  helix: -2.98 (0.17), residues: 385
  sheet: -0.65 (0.53), residues: 69
  loop : -2.98 (0.22), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 477 
 HIS   0.005   0.001   HIS D 374 
 PHE   0.018   0.001   PHE B 512 
 TYR   0.013   0.001   TYR D 183 
 ARG   0.002   0.000   ARG D 514 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 204
  time to evaluate  : 0.963 
Fit side-chains
REVERT: A  362 TYR cc_start: 0.8789 (m-80) cc_final: 0.8561 (m-80)
REVERT: A  436 ASN cc_start: 0.8211 (t0) cc_final: 0.8009 (t0)
REVERT: B  383 LYS cc_start: 0.1328 (pttp) cc_final: 0.0891 (mtmt)
REVERT: B  415 ILE cc_start: 0.7493 (mm) cc_final: 0.7243 (pp)
REVERT: D  126 ILE cc_start: 0.7831 (mt) cc_final: 0.7627 (mt)
REVERT: D  271 TRP cc_start: 0.8191 (m-90) cc_final: 0.7452 (m-90)
REVERT: D  362 THR cc_start: 0.7658 (m) cc_final: 0.7363 (m)
REVERT: D  527 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6923 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 205
  average time/residue: 1.1226
  time to fit residues: 245.1084
Evaluate side-chains
  170 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 1.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  515 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0980
   chunk 49 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0570
   chunk 45 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0970
   overall best weight:    0.3096

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

Flipped N/Q/H residues before XYZ refinement:
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 414 ASN
A 445 ASN
A 471 GLN
A 478 ASN
B 357 ASN
B 457 ASN
B 484 ASN
D  33 ASN
D  51 ASN
** D  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  61 ASN
D 154 ASN
D 194 ASN
D 221 GLN
D 277 ASN
D 300 GLN
D 378 HIS
D 505 HIS
D 522 GLN
D 531 GLN
D 599 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.175598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.146334 restraints weight = 11488.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 2.07
r_work: 0.3742 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3593 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8279  Z= 0.242
  Angle     :  0.585  10.550  11247  Z= 0.291
  Chirality :  0.046   0.298   1197
  Planarity :  0.005   0.053   1448
  Dihedral  : 13.197  98.704   1221
  Min Nonbonded Distance : 1.837

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.79 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.11 %
    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: -2.68 (0.24), residues: 968
  helix: -1.43 (0.23), residues: 403
  sheet: -0.47 (0.58), residues: 72
  loop : -2.29 (0.25), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 433 
 HIS   0.008   0.001   HIS D  34 
 PHE   0.018   0.002   PHE D 314 
 TYR   0.017   0.002   TYR A 393 
 ARG   0.007   0.001   ARG D 192 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 188
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
REVERT: A  354 ARG cc_start: 0.8505 (ttp80) cc_final: 0.8153 (ttp80)
REVERT: B  383 LYS cc_start: 0.2054 (pttp) cc_final: 0.0966 (mtmt)
REVERT: D   82 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7037 (mtp)
REVERT: D  117 ASN cc_start: 0.8286 (m-40) cc_final: 0.7997 (m-40)
REVERT: D  145 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6255 (pm20)
REVERT: D  152 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.6136 (ttp)
REVERT: D  571 GLU cc_start: 0.7506 (pt0) cc_final: 0.7303 (pt0)
  outliers start: 16
  outliers final: 6
  residues processed: 196
  average time/residue: 1.2313
  time to fit residues: 256.0045
Evaluate side-chains
  193 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 184
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 ARG
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  474 ASN
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain D residue   82 MET
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  151 ILE
Chi-restraints excluded: chain D residue  152 MET
Chi-restraints excluded: chain D residue  401 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0270
   chunk 56 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 1 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 414 ASN
B 391 ASN
B 503 GLN
** D  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 121 ASN
D 194 ASN
D 239 HIS
D 505 HIS
D 531 GLN
D 599 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.170863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.139993 restraints weight = 11372.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 2.08
r_work: 0.3634 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.3474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075   8279  Z= 0.357
  Angle     :  0.622   9.174  11247  Z= 0.313
  Chirality :  0.047   0.236   1197
  Planarity :  0.005   0.044   1448
  Dihedral  : 11.587  97.073   1219
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.41 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.11 %
    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: -2.13 (0.25), residues: 968
  helix: -0.87 (0.25), residues: 415
  sheet: -0.18 (0.60), residues: 70
  loop : -2.11 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 477 
 HIS   0.008   0.002   HIS A 502 
 PHE   0.024   0.002   PHE D 523 
 TYR   0.024   0.002   TYR D 385 
 ARG   0.007   0.001   ARG D 192 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 185
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7665 (pt)
REVERT: B  383 LYS cc_start: 0.3164 (pttp) cc_final: 0.0915 (mtmt)
REVERT: D   52 THR cc_start: 0.8425 (m) cc_final: 0.8206 (m)
REVERT: D   62 MET cc_start: 0.8400 (ttp) cc_final: 0.8159 (ttt)
REVERT: D  102 GLN cc_start: 0.6520 (OUTLIER) cc_final: 0.5707 (pp30)
REVERT: D  117 ASN cc_start: 0.8301 (m-40) cc_final: 0.8029 (m-40)
REVERT: D  215 TYR cc_start: 0.8166 (m-80) cc_final: 0.7722 (m-80)
REVERT: D  225 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7746 (m-30)
REVERT: D  363 LYS cc_start: 0.8134 (mmpt) cc_final: 0.7897 (mmpt)
REVERT: D  557 MET cc_start: 0.8757 (tmm) cc_final: 0.8517 (tmm)
REVERT: D  571 GLU cc_start: 0.7851 (pt0) cc_final: 0.7398 (pt0)
  outliers start: 28
  outliers final: 7
  residues processed: 194
  average time/residue: 1.2426
  time to fit residues: 255.0752
Evaluate side-chains
  181 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 171
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 ARG
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  474 ASN
Chi-restraints excluded: chain B residue  385 ASN
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  102 GLN
Chi-restraints excluded: chain D residue  225 ASP
Chi-restraints excluded: chain D residue  401 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 46 optimal weight:    0.4980
   chunk 94 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 33 optimal weight:    0.1980
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 75 optimal weight:    0.5980
   chunk 87 optimal weight:    0.1980
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 406 GLN
** D  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 GLN
D 175 GLN
D 194 ASN
D 552 GLN
D 599 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.166279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.134161 restraints weight = 11177.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.15
r_work: 0.3616 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.3782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   8279  Z= 0.301
  Angle     :  0.576   7.489  11247  Z= 0.289
  Chirality :  0.046   0.247   1197
  Planarity :  0.004   0.043   1448
  Dihedral  : 11.007  96.003   1219
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 16.69 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.11 %
    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: -1.72 (0.26), residues: 968
  helix: -0.39 (0.26), residues: 404
  sheet: -0.02 (0.60), residues: 70
  loop : -1.99 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 477 
 HIS   0.008   0.002   HIS D 241 
 PHE   0.018   0.001   PHE D 523 
 TYR   0.019   0.001   TYR D 385 
 ARG   0.008   0.001   ARG D 192 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 170
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  365 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7145 (pt)
REVERT: D   52 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8218 (m)
REVERT: D  102 GLN cc_start: 0.6517 (OUTLIER) cc_final: 0.5687 (pp30)
REVERT: D  117 ASN cc_start: 0.8285 (m-40) cc_final: 0.8015 (m-40)
REVERT: D  215 TYR cc_start: 0.8218 (m-80) cc_final: 0.7861 (m-80)
REVERT: D  225 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7761 (m-30)
REVERT: D  234 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8372 (mtmm)
REVERT: D  363 LYS cc_start: 0.8184 (mmpt) cc_final: 0.7892 (mmpt)
REVERT: D  557 MET cc_start: 0.8751 (tmm) cc_final: 0.8456 (tmm)
REVERT: D  571 GLU cc_start: 0.7891 (pt0) cc_final: 0.7545 (pt0)
  outliers start: 32
  outliers final: 10
  residues processed: 185
  average time/residue: 1.1778
  time to fit residues: 232.1155
Evaluate side-chains
  188 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 174
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 ARG
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  474 ASN
Chi-restraints excluded: chain A residue  522 CYS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  102 GLN
Chi-restraints excluded: chain D residue  225 ASP
Chi-restraints excluded: chain D residue  330 ASN
Chi-restraints excluded: chain D residue  401 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 93 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0980
   chunk 6 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 502 HIS
** D  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 GLN
D 175 GLN
D 194 ASN
D 388 GLN
D 599 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.167277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.135012 restraints weight = 11125.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 2.19
r_work: 0.3599 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.4073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077   8279  Z= 0.352
  Angle     :  0.584   7.774  11247  Z= 0.294
  Chirality :  0.047   0.245   1197
  Planarity :  0.004   0.053   1448
  Dihedral  : 10.622  91.805   1219
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 17.15 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.11 %
    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: -1.51 (0.26), residues: 968
  helix: -0.23 (0.26), residues: 407
  sheet:  0.10 (0.60), residues: 72
  loop : -1.88 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 477 
 HIS   0.009   0.002   HIS D 241 
 PHE   0.018   0.001   PHE A 389 
 TYR   0.020   0.002   TYR D 385 
 ARG   0.012   0.001   ARG A 354 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 184
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8604 (ttmm)
REVERT: A  365 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7359 (pt)
REVERT: A  424 ASP cc_start: 0.7743 (m-30) cc_final: 0.7469 (m-30)
REVERT: B  383 LYS cc_start: 0.3296 (pttp) cc_final: 0.0974 (mtmt)
REVERT: D   23 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7507 (mp0)
REVERT: D  102 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.5839 (pp30)
REVERT: D  117 ASN cc_start: 0.8277 (m-40) cc_final: 0.8015 (m-40)
REVERT: D  215 TYR cc_start: 0.8301 (m-80) cc_final: 0.8019 (m-80)
REVERT: D  225 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7774 (m-30)
REVERT: D  347 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8142 (p)
REVERT: D  363 LYS cc_start: 0.8177 (mmpt) cc_final: 0.7871 (mmpt)
REVERT: D  465 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7946 (ttmm)
REVERT: D  557 MET cc_start: 0.8818 (tmm) cc_final: 0.8514 (tmm)
  outliers start: 33
  outliers final: 14
  residues processed: 197
  average time/residue: 1.1924
  time to fit residues: 249.5623
Evaluate side-chains
  199 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 180
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 ARG
Chi-restraints excluded: chain A residue  346 SER
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  474 ASN
Chi-restraints excluded: chain A residue  522 CYS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain D residue   89 GLN
Chi-restraints excluded: chain D residue  102 GLN
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  225 ASP
Chi-restraints excluded: chain D residue  332 MET
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  574 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 57 optimal weight:    0.1980
   chunk 41 optimal weight:    0.9980
   chunk 14 optimal weight:    0.2980
   chunk 94 optimal weight:    0.2980
   chunk 72 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0570
   chunk 42 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.2898

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

Flipped N/Q/H residues before XYZ refinement:
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 175 GLN
D 194 ASN
D 599 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.167405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135529 restraints weight = 11152.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 2.16
r_work: 0.3619 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3463 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.4108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8279  Z= 0.216
  Angle     :  0.551   9.377  11247  Z= 0.274
  Chirality :  0.045   0.259   1197
  Planarity :  0.004   0.048   1448
  Dihedral  : 10.180  88.423   1219
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.66 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.11 %
    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: -1.30 (0.26), residues: 968
  helix: -0.02 (0.27), residues: 406
  sheet:  0.23 (0.60), residues: 72
  loop : -1.79 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 477 
 HIS   0.007   0.001   HIS D 241 
 PHE   0.020   0.001   PHE A 389 
 TYR   0.021   0.001   TYR D 202 
 ARG   0.011   0.001   ARG D 192 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 173
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8583 (ttmm)
REVERT: A  400 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7383 (ptm160)
REVERT: B  383 LYS cc_start: 0.3320 (pttp) cc_final: 0.1012 (mtmt)
REVERT: D  117 ASN cc_start: 0.8277 (m-40) cc_final: 0.8012 (m-40)
REVERT: D  215 TYR cc_start: 0.8240 (m-80) cc_final: 0.7923 (m-80)
REVERT: D  225 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7746 (m-30)
REVERT: D  347 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8196 (p)
REVERT: D  363 LYS cc_start: 0.8213 (mmpt) cc_final: 0.7871 (mmpt)
REVERT: D  401 HIS cc_start: 0.8974 (OUTLIER) cc_final: 0.8370 (m-70)
REVERT: D  465 LYS cc_start: 0.8130 (ttmm) cc_final: 0.7907 (ttmm)
REVERT: D  557 MET cc_start: 0.8804 (tmm) cc_final: 0.8523 (tmm)
  outliers start: 24
  outliers final: 8
  residues processed: 182
  average time/residue: 1.2433
  time to fit residues: 239.7568
Evaluate side-chains
  183 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  400 ARG
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  474 ASN
Chi-restraints excluded: chain A residue  522 CYS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  225 ASP
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  401 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 57 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 70 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0370
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
D 599 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.167273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.134920 restraints weight = 11161.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.20
r_work: 0.3597 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3439 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.4291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   8279  Z= 0.328
  Angle     :  0.593   8.937  11247  Z= 0.295
  Chirality :  0.047   0.268   1197
  Planarity :  0.004   0.052   1448
  Dihedral  :  9.882  84.271   1219
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 19.47 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.11 %
    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: -1.30 (0.26), residues: 968
  helix: -0.04 (0.27), residues: 409
  sheet:  0.18 (0.60), residues: 70
  loop : -1.77 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 477 
 HIS   0.008   0.001   HIS D 241 
 PHE   0.019   0.001   PHE A 389 
 TYR   0.021   0.001   TYR D 202 
 ARG   0.012   0.001   ARG D 192 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8623 (ttmm)
REVERT: D  117 ASN cc_start: 0.8301 (m-40) cc_final: 0.8014 (m-40)
REVERT: D  215 TYR cc_start: 0.8324 (m-80) cc_final: 0.8040 (m-80)
REVERT: D  225 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7795 (m-30)
REVERT: D  347 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8208 (p)
REVERT: D  363 LYS cc_start: 0.8235 (mmpt) cc_final: 0.7894 (mmpt)
REVERT: D  465 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7934 (ttmm)
REVERT: D  557 MET cc_start: 0.8836 (tmm) cc_final: 0.8513 (tmm)
  outliers start: 23
  outliers final: 10
  residues processed: 181
  average time/residue: 1.2092
  time to fit residues: 232.2351
Evaluate side-chains
  187 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 174
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 ARG
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  474 ASN
Chi-restraints excluded: chain A residue  522 CYS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  225 ASP
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  401 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 79 optimal weight:    0.5980
   chunk 80 optimal weight:    0.2980
   chunk 50 optimal weight:    0.4980
   chunk 21 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0870
   chunk 10 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 9 optimal weight:    0.3980
   chunk 84 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.3758

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

Flipped N/Q/H residues before XYZ refinement:
** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 121 ASN
D 175 GLN
D 599 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.167209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.135127 restraints weight = 11293.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 2.19
r_work: 0.3610 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3452 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.4345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8279  Z= 0.262
  Angle     :  0.575   7.984  11247  Z= 0.285
  Chirality :  0.046   0.274   1197
  Planarity :  0.004   0.058   1448
  Dihedral  :  9.458  79.695   1219
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.51 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.11 %
    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 (0.26), residues: 968
  helix:  0.04 (0.27), residues: 408
  sheet:  0.30 (0.60), residues: 72
  loop : -1.72 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 477 
 HIS   0.006   0.001   HIS D 241 
 PHE   0.021   0.001   PHE A 389 
 TYR   0.022   0.001   TYR D 202 
 ARG   0.013   0.001   ARG D 192 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8619 (ttmm)
REVERT: A  400 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7390 (ptm160)
REVERT: A  514 LEU cc_start: 0.7535 (tp) cc_final: 0.7303 (tp)
REVERT: B  383 LYS cc_start: 0.3221 (pttp) cc_final: 0.0933 (mtmt)
REVERT: D  117 ASN cc_start: 0.8284 (m-40) cc_final: 0.7998 (m-40)
REVERT: D  215 TYR cc_start: 0.8306 (m-80) cc_final: 0.8013 (m-80)
REVERT: D  225 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7782 (m-30)
REVERT: D  347 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8209 (p)
REVERT: D  363 LYS cc_start: 0.8234 (mmpt) cc_final: 0.7897 (mmpt)
REVERT: D  465 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7916 (ttmm)
REVERT: D  557 MET cc_start: 0.8833 (tmm) cc_final: 0.8547 (tmm)
  outliers start: 18
  outliers final: 9
  residues processed: 177
  average time/residue: 1.1973
  time to fit residues: 224.6232
Evaluate side-chains
  179 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 166
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  400 ARG
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  474 ASN
Chi-restraints excluded: chain A residue  522 CYS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain D residue   68 LYS
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  225 ASP
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  401 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:    0.0470
   chunk 41 optimal weight:    0.5980
   chunk 42 optimal weight:    0.2980
   chunk 67 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    0.3980
   chunk 91 optimal weight:    0.1980
   chunk 66 optimal weight:    0.0980
   chunk 29 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0010
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.1284

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

Flipped N/Q/H residues before XYZ refinement:
D 121 ASN
D 599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.170402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.138956 restraints weight = 11492.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.20
r_work: 0.3642 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3486 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8279  Z= 0.156
  Angle     :  0.541   9.943  11247  Z= 0.267
  Chirality :  0.044   0.269   1197
  Planarity :  0.004   0.052   1448
  Dihedral  :  8.866  73.541   1219
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 20.97 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.11 %
    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 (0.27), residues: 968
  helix:  0.24 (0.27), residues: 406
  sheet:  0.43 (0.61), residues: 72
  loop : -1.61 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 433 
 HIS   0.007   0.001   HIS D  34 
 PHE   0.023   0.001   PHE A 389 
 TYR   0.022   0.001   TYR D 202 
 ARG   0.014   0.001   ARG D 192 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 174
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8578 (ttmm)
REVERT: A  514 LEU cc_start: 0.7517 (tp) cc_final: 0.7282 (tp)
REVERT: B  383 LYS cc_start: 0.3136 (pttp) cc_final: 0.0891 (mtmt)
REVERT: D   58 ASN cc_start: 0.7848 (m110) cc_final: 0.7531 (m110)
REVERT: D  117 ASN cc_start: 0.8266 (m-40) cc_final: 0.8000 (m-40)
REVERT: D  215 TYR cc_start: 0.8233 (m-80) cc_final: 0.7944 (m-80)
REVERT: D  225 ASP cc_start: 0.8049 (t0) cc_final: 0.7733 (m-30)
REVERT: D  363 LYS cc_start: 0.8199 (mmpt) cc_final: 0.7856 (mmpt)
REVERT: D  401 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.8431 (m-70)
REVERT: D  465 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7856 (ttmm)
REVERT: D  557 MET cc_start: 0.8800 (tmm) cc_final: 0.8531 (tmm)
  outliers start: 11
  outliers final: 9
  residues processed: 180
  average time/residue: 1.1910
  time to fit residues: 227.2455
Evaluate side-chains
  180 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 169
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  474 ASN
Chi-restraints excluded: chain A residue  522 CYS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  151 ILE
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  401 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 3 optimal weight:    0.1980
   chunk 93 optimal weight:    0.4980
   chunk 92 optimal weight:    0.0870
   chunk 81 optimal weight:    0.2980
   chunk 45 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0870
   chunk 0 optimal weight:    0.0970
   chunk 80 optimal weight:    0.0870
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.1112

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

Flipped N/Q/H residues before XYZ refinement:
D 599 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.171911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.141776 restraints weight = 11325.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 2.08
r_work: 0.3658 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.4261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8279  Z= 0.150
  Angle     :  0.528   9.145  11247  Z= 0.261
  Chirality :  0.043   0.242   1197
  Planarity :  0.004   0.064   1448
  Dihedral  :  8.171  63.826   1219
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 21.67 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.11 %
    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: -0.83 (0.27), residues: 968
  helix:  0.41 (0.27), residues: 403
  sheet:  0.48 (0.61), residues: 72
  loop : -1.57 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 433 
 HIS   0.006   0.001   HIS D  34 
 PHE   0.019   0.001   PHE A 389 
 TYR   0.023   0.001   TYR D 202 
 ARG   0.015   0.001   ARG D 192 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 170
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  383 LYS cc_start: 0.3151 (pttp) cc_final: 0.1011 (mtmt)
REVERT: D   58 ASN cc_start: 0.7842 (m110) cc_final: 0.7511 (m110)
REVERT: D   87 GLU cc_start: 0.7308 (mp0) cc_final: 0.6943 (mm-30)
REVERT: D  117 ASN cc_start: 0.8229 (m-40) cc_final: 0.7953 (m-40)
REVERT: D  215 TYR cc_start: 0.8161 (m-80) cc_final: 0.7842 (m-80)
REVERT: D  225 ASP cc_start: 0.7960 (t0) cc_final: 0.7655 (m-30)
REVERT: D  363 LYS cc_start: 0.8161 (mmpt) cc_final: 0.7841 (mmpt)
REVERT: D  401 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8452 (m-70)
REVERT: D  465 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7854 (ttmm)
REVERT: D  557 MET cc_start: 0.8781 (tmm) cc_final: 0.8490 (tmm)
  outliers start: 11
  outliers final: 7
  residues processed: 176
  average time/residue: 1.2673
  time to fit residues: 236.0364
Evaluate side-chains
  173 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 165
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  467 THR
Chi-restraints excluded: chain A residue  474 ASN
Chi-restraints excluded: chain A residue  522 CYS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain D residue  145 GLU
Chi-restraints excluded: chain D residue  401 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 35 optimal weight:    0.3980
   chunk 94 optimal weight:    0.9990
   chunk 71 optimal weight:    0.5980
   chunk 58 optimal weight:    0.3980
   chunk 70 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 9 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
D 599 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.167540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.135277 restraints weight = 11282.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 2.20
r_work: 0.3608 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.4436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8279  Z= 0.293
  Angle     :  0.582  10.332  11247  Z= 0.289
  Chirality :  0.046   0.206   1197
  Planarity :  0.004   0.062   1448
  Dihedral  :  7.923  57.305   1219
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 21.55 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.11 %
    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: -0.89 (0.27), residues: 968
  helix:  0.29 (0.27), residues: 409
  sheet:  0.50 (0.61), residues: 72
  loop : -1.56 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 350 
 HIS   0.007   0.001   HIS D 241 
 PHE   0.017   0.001   PHE A 389 
 TYR   0.023   0.002   TYR D 202 
 ARG   0.016   0.001   ARG D 192 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8733.13 seconds
wall clock time: 154 minutes 37.60 seconds (9277.60 seconds total)