Starting phenix.real_space_refine
on Fri Aug 22 17:26:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8aqt_15589/08_2025/8aqt_15589.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8aqt_15589/08_2025/8aqt_15589.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8aqt_15589/08_2025/8aqt_15589.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8aqt_15589/08_2025/8aqt_15589.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8aqt_15589/08_2025/8aqt_15589.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8aqt_15589/08_2025/8aqt_15589.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.049
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4033      2.51       5
     N    1055      2.21       5
     O    1196      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6321
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4744
          Classifications: {'peptide': 584}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 557}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 1535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1535
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 10, 'TRANS': 182}
    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: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.81, per 1000 atoms: 0.29
  Number of scatterers: 6321
  At special positions: 0
  Unit cell: (86.086, 91.3836, 116.547, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1196      8.00
     N    1055      7.00
     C    4033      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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-ASN
      " NAG B1301 " - " ASN B 343 "
      " NAG C   1 " - " ASN A  53 "
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 341.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1466

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 2 sheets defined
      48.9% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 53
    Processing helix  chain 'A' and resid 56 through 80
    Processing helix  chain 'A' and resid 93 through 102
    Processing helix  chain 'A' and resid 111 through 117
      removed outlier: 3.623A  pdb=" N   GLN A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 129
      removed outlier: 4.350A  pdb=" N   ILE A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   TYR A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER A 128 " --> pdb=" O   SER A 124 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   THR A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 153
      removed outlier: 4.222A  pdb=" N   GLU A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 173
      removed outlier: 3.509A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 187
      removed outlier: 3.847A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 193
    Processing helix  chain 'A' and resid 198 through 205
      removed outlier: 3.827A  pdb=" N   TRP A 203 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ARG A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 230
      removed outlier: 3.592A  pdb=" N   GLU A 224 " --> pdb=" O   ASN A 220 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLU A 227 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ARG A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR A 229 " --> pdb=" O   ASP A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 4.030A  pdb=" N   GLU A 238 " --> pdb=" O   LYS A 234 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   HIS A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 234 through 239'
    Processing helix  chain 'A' and resid 239 through 252
      removed outlier: 3.756A  pdb=" N   TYR A 243 " --> pdb=" O   HIS A 239 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG A 245 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ARG A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   LYS A 247 " --> pdb=" O   TYR A 243 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LEU A 248 " --> pdb=" O   VAL A 244 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ASP A 250 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   TYR A 252 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 298
    Processing helix  chain 'A' and resid 303 through 308
      removed outlier: 3.503A  pdb=" N   PHE A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 319
      removed outlier: 4.330A  pdb=" N   GLU A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   SER A 317 " --> pdb=" O   LYS A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 330
      removed outlier: 3.733A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 383
      removed outlier: 4.368A  pdb=" N   LEU A 370 " --> pdb=" O   MET A 366 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   HIS A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   HIS A 378 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ILE A 379 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN A 380 " --> pdb=" O   MET A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 4.070A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
      removed outlier: 4.076A  pdb=" N   ILE A 421 " --> pdb=" O   HIS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 446
      removed outlier: 3.995A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   LYS A 441 " --> pdb=" O   ASN A 437 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   GLN A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE A 446 " --> pdb=" O   GLN A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 464
      removed outlier: 3.682A  pdb=" N   LYS A 458 " --> pdb=" O   TYR A 454 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   PHE A 464 " --> pdb=" O   ARG A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 485
      removed outlier: 3.645A  pdb=" N   LYS A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 531
      removed outlier: 4.258A  pdb=" N   ARG A 518 " --> pdb=" O   ARG A 514 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   ILE A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   TYR A 521 " --> pdb=" O   THR A 517 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLN A 522 " --> pdb=" O   ARG A 518 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 559
      removed outlier: 3.777A  pdb=" N   LYS A 556 " --> pdb=" O   GLN A 552 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 3.968A  pdb=" N   GLU A 564 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
    Processing helix  chain 'A' and resid 581 through 589
      removed outlier: 3.721A  pdb=" N   PHE A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 598
      removed outlier: 3.934A  pdb=" N   GLN A 598 " --> pdb=" O   TRP A 594 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 4.210A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 388
      removed outlier: 3.875A  pdb=" N   ASN B 388 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 408
      removed outlier: 4.241A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 405 through 408'
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 349
      removed outlier: 3.885A  pdb=" N   THR A 347 " --> pdb=" O   LYS A 359 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LYS A 359 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   TRP A 349 " --> pdb=" O   ARG A 357 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ARG A 357 " --> pdb=" O   TRP A 349 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 356 through 358
      removed outlier: 3.597A  pdb=" N   LYS B 356 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   TYR B 396 " --> pdb=" O   SER B 514 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE B 402 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE B 434 " --> pdb=" O   VAL B 511 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   CYS B 432 " --> pdb=" O   LEU B 513 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   VAL B 433 " --> pdb=" O   LYS B 378 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LYS B 378 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)

    191 hydrogen bonds defined for protein.
    564 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.77

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1476
        1.33 -     1.45: 1554
        1.45 -     1.58: 3405
        1.58 -     1.70: 1
        1.70 -     1.82: 58
  Bond restraints: 6494
  Sorted by residual:
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.476 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" CA  SER B 477 "
       pdb=" CB  SER B 477 "
    ideal  model  delta    sigma   weight residual
    1.530  1.486  0.044 1.69e-02 3.50e+03 6.75e+00
  bond pdb=" C   PRO B 479 "
       pdb=" O   PRO B 479 "
    ideal  model  delta    sigma   weight residual
    1.235  1.208  0.027 1.30e-02 5.92e+03 4.40e+00
  bond pdb=" CB  PRO A 389 "
       pdb=" CG  PRO A 389 "
    ideal  model  delta    sigma   weight residual
    1.492  1.578 -0.086 5.00e-02 4.00e+02 2.95e+00
  bond pdb=" N   THR B 478 "
       pdb=" CA  THR B 478 "
    ideal  model  delta    sigma   weight residual
    1.457  1.479 -0.022 1.41e-02 5.03e+03 2.44e+00
  ... (remaining 6489 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 8664
        2.27 -     4.53: 133
        4.53 -     6.80: 17
        6.80 -     9.06: 4
        9.06 -    11.33: 1
  Bond angle restraints: 8819
  Sorted by residual:
  angle pdb=" C   PRO B 479 "
        pdb=" CA  PRO B 479 "
        pdb=" CB  PRO B 479 "
      ideal   model   delta    sigma   weight residual
     111.56  100.23   11.33 1.65e+00 3.67e-01 4.71e+01
  angle pdb=" N   PRO B 479 "
        pdb=" CA  PRO B 479 "
        pdb=" C   PRO B 479 "
      ideal   model   delta    sigma   weight residual
     112.47  121.36   -8.89 2.06e+00 2.36e-01 1.86e+01
  angle pdb=" N   GLN A 287 "
        pdb=" CA  GLN A 287 "
        pdb=" C   GLN A 287 "
      ideal   model   delta    sigma   weight residual
     114.31  109.56    4.75 1.29e+00 6.01e-01 1.35e+01
  angle pdb=" N   PRO A 389 "
        pdb=" CA  PRO A 389 "
        pdb=" C   PRO A 389 "
      ideal   model   delta    sigma   weight residual
     112.47  119.46   -6.99 2.06e+00 2.36e-01 1.15e+01
  angle pdb=" C   ILE A 468 "
        pdb=" CA  ILE A 468 "
        pdb=" CB  ILE A 468 "
      ideal   model   delta    sigma   weight residual
     109.33  112.46   -3.13 9.80e-01 1.04e+00 1.02e+01
  ... (remaining 8814 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.45: 3664
       24.45 -    48.90: 187
       48.90 -    73.36: 28
       73.36 -    97.81: 3
       97.81 -   122.26: 3
  Dihedral angle restraints: 3885
    sinusoidal: 1600
      harmonic: 2285
  Sorted by residual:
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.68  -63.68     1      1.00e+01 1.00e-02 5.34e+01
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.48   53.48     1      1.00e+01 1.00e-02 3.89e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.79   53.21     1      1.00e+01 1.00e-02 3.85e+01
  ... (remaining 3882 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 730
       0.050 -    0.101: 170
       0.101 -    0.151: 26
       0.151 -    0.201: 2
       0.201 -    0.252: 1
  Chirality restraints: 929
  Sorted by residual:
  chirality pdb=" CA  PRO A 389 "
            pdb=" N   PRO A 389 "
            pdb=" C   PRO A 389 "
            pdb=" CB  PRO A 389 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" C2  NAG C   2 "
            pdb=" C1  NAG C   2 "
            pdb=" C3  NAG C   2 "
            pdb=" N2  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.33   -0.16 2.00e-01 2.50e+01 6.43e-01
  chirality pdb=" CA  CYS B 480 "
            pdb=" N   CYS B 480 "
            pdb=" C   CYS B 480 "
            pdb=" CB  CYS B 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.15 2.00e-01 2.50e+01 6.01e-01
  ... (remaining 926 not shown)

  Planarity restraints: 1144
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 388 "    0.081 5.00e-02 4.00e+02   1.22e-01 2.40e+01
        pdb=" N   PRO A 389 "   -0.212 5.00e-02 4.00e+02
        pdb=" CA  PRO A 389 "    0.068 5.00e-02 4.00e+02
        pdb=" CD  PRO A 389 "    0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 475 "   -0.012 2.00e-02 2.50e+03   2.53e-02 6.39e+00
        pdb=" C   ALA B 475 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ALA B 475 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLY B 476 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 468 "    0.036 5.00e-02 4.00e+02   5.49e-02 4.82e+00
        pdb=" N   PRO A 469 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 469 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 469 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1141 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 207
        2.71 -     3.26: 6506
        3.26 -     3.81: 9278
        3.81 -     4.35: 11190
        4.35 -     4.90: 17785
  Nonbonded interactions: 44966
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 370 "
            pdb=" ND1 HIS A 374 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" OG1 THR B 500 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OE2 GLU A 227 "
            pdb=" OH  TYR A 454 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   LEU A 278 "
            pdb=" OG1 THR A 282 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" NZ  LYS A 247 "
            pdb=" O   LEU A 281 "
     model   vdw
     2.240 3.120
  ... (remaining 44961 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.110
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5934
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086   6503  Z= 0.163
  Angle     :  0.705  11.326   8840  Z= 0.395
  Chirality :  0.044   0.252    929
  Planarity :  0.006   0.122   1142
  Dihedral  : 14.457 122.259   2401
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.78 %
    Allowed  :  5.43 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  0.15 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.29), residues: 773
  helix: -0.56 (0.30), residues: 297
  sheet:  2.44 (1.08), residues: 22
  loop : -1.91 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 161 
 TYR   0.009   0.001   TYR A 215 
 PHE   0.016   0.001   PHE A 390 
 TRP   0.016   0.002   TRP A  48 
 HIS   0.006   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6494)
  covalent geometry    : angle       0.69510 ( 8819)
  SS BOND              : bond        0.00345 (    6)
  SS BOND              : angle       1.09912 (   12)
  hydrogen bonds       : bond        0.16052 (  191)
  hydrogen bonds       : angle       6.77141 (  564)
  link_BETA1-4         : bond        0.00013 (    1)
  link_BETA1-4         : angle       4.42955 (    3)
  link_NAG-ASN         : bond        0.00396 (    2)
  link_NAG-ASN         : angle       2.98636 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 170
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.8580 (mt0) cc_final: 0.8256 (mt0)
REVERT: A   74 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7626 (tm-30)
REVERT: A  190 MET cc_start: 0.7766 (tpp) cc_final: 0.7410 (ppp)
REVERT: A  461 TRP cc_start: 0.7929 (m-10) cc_final: 0.7545 (m-10)
REVERT: A  539 LEU cc_start: 0.7599 (mt) cc_final: 0.7328 (tp)
REVERT: B  386 LYS cc_start: 0.9115 (pttm) cc_final: 0.8733 (tttm)
REVERT: B  421 TYR cc_start: 0.8677 (m-80) cc_final: 0.8354 (m-80)
REVERT: B  466 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7392 (mmm160)
  outliers start: 3
  outliers final: 3
  residues processed: 173
  average time/residue: 0.0864
  time to fit residues: 19.4110
Evaluate side-chains
  96 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 188 ASN
A 508 ASN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.141583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.125838 restraints weight = 31528.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.127981 restraints weight = 22700.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.129619 restraints weight = 17512.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.130785 restraints weight = 14101.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.131645 restraints weight = 11848.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6137
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   6503  Z= 0.139
  Angle     :  0.676   9.307   8840  Z= 0.339
  Chirality :  0.047   0.327    929
  Planarity :  0.006   0.122   1142
  Dihedral  :  9.058 110.736    913
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.08 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  5.19 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.66 (0.29), residues: 773
  helix: -0.33 (0.31), residues: 285
  sheet:  1.45 (1.07), residues: 25
  loop : -1.83 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 509 
 TYR   0.011   0.001   TYR A 215 
 PHE   0.034   0.002   PHE A 592 
 TRP   0.011   0.001   TRP A 459 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6494)
  covalent geometry    : angle       0.66284 ( 8819)
  SS BOND              : bond        0.00290 (    6)
  SS BOND              : angle       2.63211 (   12)
  hydrogen bonds       : bond        0.03937 (  191)
  hydrogen bonds       : angle       5.55941 (  564)
  link_BETA1-4         : bond        0.00431 (    1)
  link_BETA1-4         : angle       3.00278 (    3)
  link_NAG-ASN         : bond        0.00215 (    2)
  link_NAG-ASN         : angle       2.92355 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8087 (m-30) cc_final: 0.7717 (m-30)
REVERT: A   74 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: A  522 GLN cc_start: 0.8764 (pt0) cc_final: 0.8552 (pt0)
REVERT: A  539 LEU cc_start: 0.8095 (mt) cc_final: 0.7407 (tp)
REVERT: A  579 MET cc_start: 0.1555 (ttp) cc_final: 0.1329 (ttt)
REVERT: B  390 LEU cc_start: 0.9107 (mt) cc_final: 0.8518 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 120
  average time/residue: 0.0778
  time to fit residues: 12.5523
Evaluate side-chains
  93 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0770
   chunk 66 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.7542

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.140342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.125519 restraints weight = 32759.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.127673 restraints weight = 23516.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.129212 restraints weight = 17971.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.130419 restraints weight = 14432.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.131210 restraints weight = 11985.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.4222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6125
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085   6503  Z= 0.122
  Angle     :  0.645   9.489   8840  Z= 0.321
  Chirality :  0.047   0.335    929
  Planarity :  0.005   0.119   1142
  Dihedral  :  8.765 108.784    913
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  4.66 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.12 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.29), residues: 773
  helix: -0.57 (0.30), residues: 296
  sheet:  1.48 (1.02), residues: 25
  loop : -1.76 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 273 
 TYR   0.016   0.001   TYR B 421 
 PHE   0.016   0.002   PHE A 314 
 TRP   0.052   0.002   TRP A 461 
 HIS   0.003   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6494)
  covalent geometry    : angle       0.63727 ( 8819)
  SS BOND              : bond        0.00530 (    6)
  SS BOND              : angle       1.44212 (   12)
  hydrogen bonds       : bond        0.03607 (  191)
  hydrogen bonds       : angle       5.23208 (  564)
  link_BETA1-4         : bond        0.00207 (    1)
  link_BETA1-4         : angle       3.24961 (    3)
  link_NAG-ASN         : bond        0.00216 (    2)
  link_NAG-ASN         : angle       2.61268 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8111 (m-30) cc_final: 0.7774 (m-30)
REVERT: A   74 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7638 (tm-30)
REVERT: A  383 MET cc_start: 0.8039 (ptp) cc_final: 0.7470 (tpt)
REVERT: A  539 LEU cc_start: 0.7806 (mt) cc_final: 0.7353 (tp)
REVERT: B  390 LEU cc_start: 0.9146 (mt) cc_final: 0.8461 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 118
  average time/residue: 0.0787
  time to fit residues: 12.2926
Evaluate side-chains
  91 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 67 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 4 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0670
   chunk 15 optimal weight:    0.6980
   chunk 25 optimal weight:    0.3980
   chunk 65 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.140530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.125193 restraints weight = 31570.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.127495 restraints weight = 22282.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.129189 restraints weight = 16773.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.130438 restraints weight = 13258.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.131398 restraints weight = 10870.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6106
moved from start:          0.3728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087   6503  Z= 0.117
  Angle     :  0.636   9.392   8840  Z= 0.313
  Chirality :  0.047   0.338    929
  Planarity :  0.005   0.117   1142
  Dihedral  :  8.412 106.326    913
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.17 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.26 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.29), residues: 773
  helix: -0.33 (0.31), residues: 287
  sheet:  1.30 (0.94), residues: 25
  loop : -1.69 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 466 
 TYR   0.011   0.001   TYR B 421 
 PHE   0.014   0.001   PHE B 374 
 TRP   0.025   0.001   TRP A 461 
 HIS   0.004   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6494)
  covalent geometry    : angle       0.62866 ( 8819)
  SS BOND              : bond        0.00236 (    6)
  SS BOND              : angle       1.45388 (   12)
  hydrogen bonds       : bond        0.03331 (  191)
  hydrogen bonds       : angle       5.17306 (  564)
  link_BETA1-4         : bond        0.00329 (    1)
  link_BETA1-4         : angle       3.37845 (    3)
  link_NAG-ASN         : bond        0.00205 (    2)
  link_NAG-ASN         : angle       2.40458 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8031 (m-30) cc_final: 0.7713 (m-30)
REVERT: A   74 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7591 (tm-30)
REVERT: A  356 PHE cc_start: 0.7700 (m-10) cc_final: 0.7458 (m-10)
REVERT: A  539 LEU cc_start: 0.7800 (mt) cc_final: 0.7179 (tp)
REVERT: B  390 LEU cc_start: 0.9117 (mt) cc_final: 0.8439 (tp)
REVERT: B  466 ARG cc_start: 0.8013 (mmm160) cc_final: 0.7797 (mmm160)
  outliers start: 1
  outliers final: 1
  residues processed: 116
  average time/residue: 0.0818
  time to fit residues: 12.3874
Evaluate side-chains
  89 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 73 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 31 optimal weight:    0.1980
   chunk 66 optimal weight:    0.0030
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:   20.0000
   chunk 4 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0270
   chunk 44 optimal weight:    0.4980
   overall best weight:    0.2448

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

Flipped N/Q/H residues before XYZ refinement:
A 417 HIS
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.142565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.127223 restraints weight = 31243.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.129692 restraints weight = 21768.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.131442 restraints weight = 16181.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.132739 restraints weight = 12657.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.133750 restraints weight = 10280.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6056
moved from start:          0.4004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085   6503  Z= 0.113
  Angle     :  0.636   9.371   8840  Z= 0.313
  Chirality :  0.047   0.336    929
  Planarity :  0.005   0.115   1142
  Dihedral  :  8.035 104.017    913
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.66 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.52 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.59 (0.29), residues: 773
  helix: -0.51 (0.30), residues: 297
  sheet:  0.88 (0.98), residues: 23
  loop : -1.58 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 273 
 TYR   0.010   0.001   TYR B 421 
 PHE   0.022   0.001   PHE A 452 
 TRP   0.017   0.001   TRP A 461 
 HIS   0.002   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6494)
  covalent geometry    : angle       0.62868 ( 8819)
  SS BOND              : bond        0.00288 (    6)
  SS BOND              : angle       1.43234 (   12)
  hydrogen bonds       : bond        0.03335 (  191)
  hydrogen bonds       : angle       4.85610 (  564)
  link_BETA1-4         : bond        0.00357 (    1)
  link_BETA1-4         : angle       3.51949 (    3)
  link_NAG-ASN         : bond        0.00346 (    2)
  link_NAG-ASN         : angle       2.17244 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8163 (m-30) cc_final: 0.7842 (m-30)
REVERT: A   74 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7986 (tm-30)
REVERT: A  356 PHE cc_start: 0.7773 (m-10) cc_final: 0.7509 (m-10)
REVERT: A  539 LEU cc_start: 0.7769 (mt) cc_final: 0.7300 (tp)
REVERT: B  390 LEU cc_start: 0.9043 (mt) cc_final: 0.8373 (tp)
REVERT: B  518 LEU cc_start: 0.8350 (tp) cc_final: 0.8042 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 116
  average time/residue: 0.0826
  time to fit residues: 12.3012
Evaluate side-chains
  89 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 59 optimal weight:    0.1980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 508 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.140271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.124974 restraints weight = 31760.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.127269 restraints weight = 22463.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.128992 restraints weight = 16916.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.130266 restraints weight = 13320.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.131224 restraints weight = 10922.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.4221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6126
moved from start:          0.4394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   6503  Z= 0.116
  Angle     :  0.652   9.356   8840  Z= 0.322
  Chirality :  0.046   0.321    929
  Planarity :  0.005   0.113   1142
  Dihedral  :  8.016 104.354    913
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.05 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  2.08 %
    Favored  : 97.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.30), residues: 773
  helix: -0.26 (0.31), residues: 291
  sheet:  1.38 (0.94), residues: 25
  loop : -1.61 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 169 
 TYR   0.008   0.001   TYR A 510 
 PHE   0.022   0.001   PHE A 452 
 TRP   0.018   0.001   TRP A 461 
 HIS   0.004   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6494)
  covalent geometry    : angle       0.64434 ( 8819)
  SS BOND              : bond        0.00192 (    6)
  SS BOND              : angle       1.65856 (   12)
  hydrogen bonds       : bond        0.03270 (  191)
  hydrogen bonds       : angle       4.93934 (  564)
  link_BETA1-4         : bond        0.00432 (    1)
  link_BETA1-4         : angle       3.39222 (    3)
  link_NAG-ASN         : bond        0.00292 (    2)
  link_NAG-ASN         : angle       2.24088 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 107
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8142 (m-30) cc_final: 0.7723 (m-30)
REVERT: A   60 GLN cc_start: 0.8571 (mp10) cc_final: 0.8260 (mp10)
REVERT: A   74 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: A  356 PHE cc_start: 0.7737 (m-10) cc_final: 0.7519 (m-10)
REVERT: A  379 ILE cc_start: 0.8772 (tp) cc_final: 0.8391 (tp)
REVERT: A  539 LEU cc_start: 0.7866 (mt) cc_final: 0.7160 (tp)
REVERT: B  390 LEU cc_start: 0.9055 (mt) cc_final: 0.8347 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 109
  average time/residue: 0.0760
  time to fit residues: 10.9470
Evaluate side-chains
  85 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0670
   chunk 65 optimal weight:    0.0050
   chunk 61 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 64 optimal weight:    4.9990
   chunk 12 optimal weight:   20.0000
   chunk 6 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    1.9936

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

Flipped N/Q/H residues before XYZ refinement:
A 221 GLN
A 239 HIS
A 442 GLN
A 505 HIS
A 508 ASN
B 448 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.134193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.118780 restraints weight = 31757.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.121043 restraints weight = 21910.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.122632 restraints weight = 16307.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.123822 restraints weight = 12822.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.124607 restraints weight = 10524.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6392
moved from start:          0.5226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   6503  Z= 0.187
  Angle     :  0.735  10.105   8840  Z= 0.374
  Chirality :  0.049   0.263    929
  Planarity :  0.006   0.115   1142
  Dihedral  :  8.848 110.309    913
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.34 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.37 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.29), residues: 773
  helix: -0.67 (0.29), residues: 301
  sheet:  0.96 (1.03), residues: 23
  loop : -1.63 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 273 
 TYR   0.012   0.002   TYR A 207 
 PHE   0.034   0.003   PHE A 452 
 TRP   0.022   0.002   TRP A 461 
 HIS   0.006   0.002   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 6494)
  covalent geometry    : angle       0.72638 ( 8819)
  SS BOND              : bond        0.00244 (    6)
  SS BOND              : angle       1.93105 (   12)
  hydrogen bonds       : bond        0.04144 (  191)
  hydrogen bonds       : angle       5.61801 (  564)
  link_BETA1-4         : bond        0.00260 (    1)
  link_BETA1-4         : angle       3.16007 (    3)
  link_NAG-ASN         : bond        0.00347 (    2)
  link_NAG-ASN         : angle       2.73181 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8101 (m-30) cc_final: 0.7703 (m-30)
REVERT: A  356 PHE cc_start: 0.7898 (m-10) cc_final: 0.7521 (m-10)
REVERT: A  557 MET cc_start: 0.5830 (mmt) cc_final: 0.5610 (mmt)
  outliers start: 1
  outliers final: 1
  residues processed: 100
  average time/residue: 0.0707
  time to fit residues: 9.3578
Evaluate side-chains
  70 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0470
   chunk 3 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 56 optimal weight:    6.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
A 373 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.144309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.131534 restraints weight = 33490.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.133405 restraints weight = 23273.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.134702 restraints weight = 17290.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.135629 restraints weight = 13590.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.136194 restraints weight = 11151.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6216
moved from start:          0.5431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   6503  Z= 0.117
  Angle     :  0.666   9.312   8840  Z= 0.327
  Chirality :  0.046   0.291    929
  Planarity :  0.005   0.113   1142
  Dihedral  :  8.313 106.456    913
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.95 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.89 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.30), residues: 773
  helix: -0.42 (0.30), residues: 304
  sheet:  1.66 (1.03), residues: 25
  loop : -1.60 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 403 
 TYR   0.008   0.001   TYR B 421 
 PHE   0.021   0.001   PHE A 452 
 TRP   0.015   0.001   TRP A 461 
 HIS   0.004   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6494)
  covalent geometry    : angle       0.65605 ( 8819)
  SS BOND              : bond        0.00174 (    6)
  SS BOND              : angle       2.19199 (   12)
  hydrogen bonds       : bond        0.03188 (  191)
  hydrogen bonds       : angle       5.04297 (  564)
  link_BETA1-4         : bond        0.00336 (    1)
  link_BETA1-4         : angle       3.30532 (    3)
  link_NAG-ASN         : bond        0.00228 (    2)
  link_NAG-ASN         : angle       2.20330 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.7988 (m-30) cc_final: 0.7515 (m-30)
REVERT: A   45 LEU cc_start: 0.8682 (mm) cc_final: 0.8474 (mm)
REVERT: A   74 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8058 (tm-30)
REVERT: A  108 LEU cc_start: 0.7224 (tt) cc_final: 0.6484 (mp)
REVERT: A  360 MET cc_start: 0.5505 (mmp) cc_final: 0.5210 (mmp)
REVERT: A  557 MET cc_start: 0.5706 (mmt) cc_final: 0.5476 (mmt)
REVERT: B  390 LEU cc_start: 0.9075 (mt) cc_final: 0.8511 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 97
  average time/residue: 0.0778
  time to fit residues: 9.9726
Evaluate side-chains
  81 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 55 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0470
   chunk 44 optimal weight:    4.9990
   chunk 31 optimal weight:    0.1980
   chunk 53 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0770
   chunk 35 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0570
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.2354

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.145520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.132807 restraints weight = 33724.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.134694 restraints weight = 23220.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.135988 restraints weight = 17067.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.136960 restraints weight = 13316.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.137616 restraints weight = 10870.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6189
moved from start:          0.5528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   6503  Z= 0.111
  Angle     :  0.653  10.164   8840  Z= 0.314
  Chirality :  0.046   0.277    929
  Planarity :  0.005   0.112   1142
  Dihedral  :  7.898 102.792    913
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.69 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  0.59 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.30), residues: 773
  helix: -0.37 (0.30), residues: 310
  sheet:  1.13 (1.03), residues: 23
  loop : -1.62 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 466 
 TYR   0.011   0.001   TYR A 510 
 PHE   0.023   0.001   PHE A 592 
 TRP   0.025   0.001   TRP A 461 
 HIS   0.002   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6494)
  covalent geometry    : angle       0.64621 ( 8819)
  SS BOND              : bond        0.00342 (    6)
  SS BOND              : angle       1.39082 (   12)
  hydrogen bonds       : bond        0.03037 (  191)
  hydrogen bonds       : angle       4.77248 (  564)
  link_BETA1-4         : bond        0.00392 (    1)
  link_BETA1-4         : angle       3.31327 (    3)
  link_NAG-ASN         : bond        0.00285 (    2)
  link_NAG-ASN         : angle       2.09536 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8126 (m-30) cc_final: 0.7747 (m-30)
REVERT: A   74 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7990 (tm-30)
REVERT: A  505 HIS cc_start: 0.7256 (OUTLIER) cc_final: 0.6885 (p90)
REVERT: A  557 MET cc_start: 0.5982 (mmt) cc_final: 0.5684 (mmt)
REVERT: A  591 LEU cc_start: 0.8087 (tt) cc_final: 0.7774 (mm)
REVERT: B  390 LEU cc_start: 0.9053 (mt) cc_final: 0.8508 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 100
  average time/residue: 0.0812
  time to fit residues: 10.7516
Evaluate side-chains
  78 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0030
   chunk 56 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0010
   chunk 72 optimal weight:    0.0020
   chunk 74 optimal weight:    0.0470
   chunk 39 optimal weight:    0.0170
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.0140

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.146731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.133805 restraints weight = 33495.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.135648 restraints weight = 23367.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.136955 restraints weight = 17393.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.137873 restraints weight = 13648.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.138602 restraints weight = 11211.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.4224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6137
moved from start:          0.5662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   6503  Z= 0.114
  Angle     :  0.670   9.479   8840  Z= 0.323
  Chirality :  0.046   0.282    929
  Planarity :  0.005   0.109   1142
  Dihedral  :  7.633  99.379    913
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.79 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.45 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.30), residues: 773
  helix: -0.36 (0.29), residues: 310
  sheet:  1.56 (1.02), residues: 25
  loop : -1.60 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 466 
 TYR   0.015   0.001   TYR B 508 
 PHE   0.020   0.001   PHE A 452 
 TRP   0.021   0.001   TRP A 461 
 HIS   0.002   0.000   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6494)
  covalent geometry    : angle       0.65991 ( 8819)
  SS BOND              : bond        0.00272 (    6)
  SS BOND              : angle       2.45534 (   12)
  hydrogen bonds       : bond        0.02946 (  191)
  hydrogen bonds       : angle       4.73063 (  564)
  link_BETA1-4         : bond        0.00476 (    1)
  link_BETA1-4         : angle       3.25967 (    3)
  link_NAG-ASN         : bond        0.00263 (    2)
  link_NAG-ASN         : angle       2.17933 (    6)

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

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

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1546 Ramachandran restraints generated.
    773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.8090 (m-30) cc_final: 0.7641 (m-30)
REVERT: A   74 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: A  360 MET cc_start: 0.4996 (mmp) cc_final: 0.4727 (mmp)
REVERT: A  591 LEU cc_start: 0.8132 (tt) cc_final: 0.7842 (mm)
REVERT: B  390 LEU cc_start: 0.9027 (mt) cc_final: 0.8500 (tp)
  outliers start: 1
  outliers final: 1
  residues processed: 99
  average time/residue: 0.0770
  time to fit residues: 10.2572
Evaluate side-chains
  82 residues out of total 677 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   chunk 68 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 505 HIS
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.143693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.130810 restraints weight = 33854.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.132647 restraints weight = 23603.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.133937 restraints weight = 17571.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.134872 restraints weight = 13763.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.135492 restraints weight = 11294.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6241
moved from start:          0.5863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   6503  Z= 0.119
  Angle     :  0.662   9.352   8840  Z= 0.321
  Chirality :  0.046   0.283    929
  Planarity :  0.005   0.109   1142
  Dihedral  :  7.811 100.580    913
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.43 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  0.30 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.30), residues: 773
  helix: -0.25 (0.29), residues: 320
  sheet:  1.11 (1.07), residues: 23
  loop : -1.71 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 466 
 TYR   0.012   0.001   TYR B 508 
 PHE   0.020   0.002   PHE A 452 
 TRP   0.018   0.001   TRP A 461 
 HIS   0.007   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6494)
  covalent geometry    : angle       0.65548 ( 8819)
  SS BOND              : bond        0.00560 (    6)
  SS BOND              : angle       1.33332 (   12)
  hydrogen bonds       : bond        0.03043 (  191)
  hydrogen bonds       : angle       4.84900 (  564)
  link_BETA1-4         : bond        0.00054 (    1)
  link_BETA1-4         : angle       3.15405 (    3)
  link_NAG-ASN         : bond        0.00274 (    2)
  link_NAG-ASN         : angle       2.19839 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1140.25 seconds
wall clock time: 20 minutes 13.19 seconds (1213.19 seconds total)