Starting phenix.real_space_refine
on Thu Jul  2 06:46:18 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7p9v_13267/07_2026/7p9v_13267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p9v_13267/07_2026/7p9v_13267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p9v_13267/07_2026/7p9v_13267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p9v_13267/07_2026/7p9v_13267.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7p9v_13267/07_2026/7p9v_13267.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7p9v_13267/07_2026/7p9v_13267.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p9v_13267/07_2026/7p9v_13267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p9v_13267/07_2026/7p9v_13267.map"
  }
  resolution = 3.4
  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=  -0.002 sd=   0.046
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      27      5.16       5
     C    4751      2.51       5
     N    1185      2.21       5
     O    1323      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7286
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3616
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 464, 3616
          Classifications: {'peptide': 464}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 441}
    Chain: "B"
      Number of atoms: 3558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 455, 3558
          Classifications: {'peptide': 455}
          Link IDs: {'PTRANS': 23, 'TRANS': 431}
    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 chiralities: 2
    Chain: "D"
      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 chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      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 chiralities: 2
  Time building chain proxies: 1.08, per 1000 atoms: 0.15
  Number of scatterers: 7286
  At special positions: 0
  Unit cell: (85.696, 79.872, 131.456, 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      27     16.00
     O    1323      8.00
     N    1185      7.00
     C    4751      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 158 " distance=2.21

  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 D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 366 "
      " NAG E   1 " - " ASN A 382 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 253.5 milliseconds
  

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1696

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 5 sheets defined
      57.5% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 168 through 175
    Processing helix  chain 'A' and resid 179 through 208
      removed outlier: 3.574A  pdb=" N   ARG A 183 " --> pdb=" O   TRP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 236
    Processing helix  chain 'A' and resid 242 through 247
    Processing helix  chain 'A' and resid 248 through 255
    Processing helix  chain 'A' and resid 283 through 286
    Processing helix  chain 'A' and resid 287 through 301
      removed outlier: 3.704A  pdb=" N   SER A 293 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LYS A 300 " --> pdb=" O   GLN A 296 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   LYS A 301 " --> pdb=" O   SER A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 342
      removed outlier: 4.336A  pdb=" N   LYS A 332 " --> pdb=" O   ALA A 328 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LEU A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 372
      removed outlier: 3.746A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
    Processing helix  chain 'A' and resid 405 through 407
      No H-bonds generated for 'chain 'A' and resid 405 through 407'
    Processing helix  chain 'A' and resid 414 through 427
      removed outlier: 4.261A  pdb=" N   VAL A 420 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   THR A 427 " --> pdb=" O   TYR A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 449
      No H-bonds generated for 'chain 'A' and resid 447 through 449'
    Processing helix  chain 'A' and resid 450 through 461
      removed outlier: 3.650A  pdb=" N   GLN A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 515
      removed outlier: 3.811A  pdb=" N   GLU A 515 " --> pdb=" O   LYS A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 534
    Processing helix  chain 'A' and resid 534 through 540
      removed outlier: 3.624A  pdb=" N   LEU A 538 " --> pdb=" O   GLU A 534 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   HIS A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 4.006A  pdb=" N   SER A 589 " --> pdb=" O   ALA A 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 58
      removed outlier: 3.809A  pdb=" N   THR B  56 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE B  58 " --> pdb=" O   ILE B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 72
      Proline residue:  B  66  - end of helix
      removed outlier: 3.602A  pdb=" N   ASN B  72 " --> pdb=" O   GLY B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 105
      removed outlier: 3.653A  pdb=" N   ILE B  82 " --> pdb=" O   MET B  78 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LYS B 105 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 116
      removed outlier: 3.899A  pdb=" N   GLU B 116 " --> pdb=" O   THR B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 133
      removed outlier: 3.618A  pdb=" N   ALA B 123 " --> pdb=" O   GLY B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 152
      removed outlier: 3.579A  pdb=" N   ALA B 145 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG B 148 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 183
      removed outlier: 3.536A  pdb=" N   ILE B 165 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS B 166 " --> pdb=" O   GLU B 162 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER B 183 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 211
      removed outlier: 3.927A  pdb=" N   ILE B 190 " --> pdb=" O   TRP B 186 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLN B 191 " --> pdb=" O   SER B 187 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE B 202 " --> pdb=" O   LYS B 198 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   ILE B 205 " --> pdb=" O   ALA B 201 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL B 207 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      Proline residue:  B 208  - end of helix
    Processing helix  chain 'B' and resid 231 through 233
      No H-bonds generated for 'chain 'B' and resid 231 through 233'
    Processing helix  chain 'B' and resid 234 through 246
      removed outlier: 3.739A  pdb=" N   ALA B 238 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   TYR B 246 " --> pdb=" O   GLY B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 292
      removed outlier: 4.365A  pdb=" N   ILE B 276 " --> pdb=" O   ILE B 272 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL B 277 " --> pdb=" O   SER B 273 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   THR B 291 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 300
    Processing helix  chain 'B' and resid 302 through 312
      removed outlier: 3.772A  pdb=" N   THR B 306 " --> pdb=" O   ALA B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 332
      removed outlier: 3.589A  pdb=" N   ALA B 318 " --> pdb=" O   ASN B 314 " (cutoff:3.500A)
      Proline residue:  B 320  - end of helix
      removed outlier: 4.944A  pdb=" N   ALA B 324 " --> pdb=" O   PRO B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 335
      No H-bonds generated for 'chain 'B' and resid 333 through 335'
    Processing helix  chain 'B' and resid 336 through 348
      removed outlier: 3.985A  pdb=" N   LEU B 341 " --> pdb=" O   ALA B 337 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG B 347 " --> pdb=" O   TYR B 343 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   GLU B 348 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 355
    Processing helix  chain 'B' and resid 365 through 370
      removed outlier: 3.536A  pdb=" N   VAL B 369 " --> pdb=" O   PRO B 365 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ILE B 370 " --> pdb=" O   LEU B 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 365 through 370'
    Processing helix  chain 'B' and resid 371 through 382
      removed outlier: 4.265A  pdb=" N   LEU B 375 " --> pdb=" O   VAL B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 402
      removed outlier: 4.271A  pdb=" N   ASN B 390 " --> pdb=" O   ASP B 386 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ALA B 395 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE B 399 " --> pdb=" O   ALA B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 411
      removed outlier: 3.858A  pdb=" N   LEU B 407 " --> pdb=" O   ALA B 403 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ILE B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   TYR B 409 " --> pdb=" O   ALA B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 439
      removed outlier: 5.537A  pdb=" N   PHE B 433 " --> pdb=" O   ALA B 429 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   THR B 434 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   PHE B 437 " --> pdb=" O   PHE B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 443
      removed outlier: 3.786A  pdb=" N   LEU B 443 " --> pdb=" O   ALA B 440 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 440 through 443'
    Processing helix  chain 'B' and resid 450 through 460
    Processing helix  chain 'B' and resid 461 through 466
      removed outlier: 3.582A  pdb=" N   TYR B 464 " --> pdb=" O   VAL B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 492
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 403
      removed outlier: 7.316A  pdb=" N   LEU A 377 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   THR A 402 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ALA A 379 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   PHE A 346 " --> pdb=" O   ILE A 378 " (cutoff:3.500A)
      removed outlier: 8.752A  pdb=" N   GLY A 380 " --> pdb=" O   PHE A 346 " (cutoff:3.500A)
      removed outlier: 8.637A  pdb=" N   GLN A 347 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ASP A 308 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268
      removed outlier: 6.171A  pdb=" N   GLN A 280 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545
      removed outlier: 3.567A  pdb=" N   PHE A 545 " --> pdb=" O   SER A 553 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 609 through 611
      removed outlier: 7.052A  pdb=" N   LEU A 624 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 357 through 359

    318 hydrogen bonds defined for protein.
    924 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: 0.71

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2252
        1.34 -     1.46: 1535
        1.46 -     1.58: 3631
        1.58 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 7463
  Sorted by residual:
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.456 -0.050 2.00e-02 2.50e+03 6.38e+00
  bond pdb=" CA  LEU A 335 "
       pdb=" C   LEU A 335 "
    ideal  model  delta    sigma   weight residual
    1.522  1.492  0.030 1.43e-02 4.89e+03 4.44e+00
  bond pdb=" C   LEU A 335 "
       pdb=" N   GLU A 336 "
    ideal  model  delta    sigma   weight residual
    1.332  1.310  0.022 1.29e-02 6.01e+03 2.96e+00
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.66e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.52e+00
  ... (remaining 7458 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 9909
        2.20 -     4.40: 209
        4.40 -     6.59: 24
        6.59 -     8.79: 6
        8.79 -    10.99: 3
  Bond angle restraints: 10151
  Sorted by residual:
  angle pdb=" N   ILE B 205 "
        pdb=" CA  ILE B 205 "
        pdb=" C   ILE B 205 "
      ideal   model   delta    sigma   weight residual
     111.90  109.22    2.68 8.10e-01 1.52e+00 1.10e+01
  angle pdb=" N   GLY B 334 "
        pdb=" CA  GLY B 334 "
        pdb=" C   GLY B 334 "
      ideal   model   delta    sigma   weight residual
     115.66  110.27    5.39 1.63e+00 3.76e-01 1.10e+01
  angle pdb=" N   LEU B 430 "
        pdb=" CA  LEU B 430 "
        pdb=" C   LEU B 430 "
      ideal   model   delta    sigma   weight residual
     114.75  110.66    4.09 1.26e+00 6.30e-01 1.05e+01
  angle pdb=" N   VAL B  76 "
        pdb=" CA  VAL B  76 "
        pdb=" C   VAL B  76 "
      ideal   model   delta    sigma   weight residual
     111.56  108.80    2.76 8.60e-01 1.35e+00 1.03e+01
  angle pdb=" CA  TRP B 476 "
        pdb=" CB  TRP B 476 "
        pdb=" CG  TRP B 476 "
      ideal   model   delta    sigma   weight residual
     113.60  107.53    6.07 1.90e+00 2.77e-01 1.02e+01
  ... (remaining 10146 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 3899
       17.85 -    35.69: 367
       35.69 -    53.54: 53
       53.54 -    71.38: 2
       71.38 -    89.23: 7
  Dihedral angle restraints: 4328
    sinusoidal: 1689
      harmonic: 2639
  Sorted by residual:
  dihedral pdb=" CA  PRO B 320 "
           pdb=" C   PRO B 320 "
           pdb=" N   ILE B 321 "
           pdb=" CA  ILE B 321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.09   21.91     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  LYS A 270 "
           pdb=" C   LYS A 270 "
           pdb=" N   ASP A 271 "
           pdb=" CA  ASP A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.58   21.42     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  ALA B 429 "
           pdb=" C   ALA B 429 "
           pdb=" N   LEU B 430 "
           pdb=" CA  LEU B 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.75   20.25     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 4325 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1125
       0.092 -    0.185: 67
       0.185 -    0.277: 2
       0.277 -    0.369: 0
       0.369 -    0.461: 1
  Chirality restraints: 1195
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 366 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.94   -0.46 2.00e-01 2.50e+01 5.32e+00
  chirality pdb=" C2  NAG D   1 "
            pdb=" C1  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" N2  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.29   -0.20 2.00e-01 2.50e+01 9.91e-01
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 425 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 9.13e-01
  ... (remaining 1192 not shown)

  Planarity restraints: 1262
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 476 "   -0.032 2.00e-02 2.50e+03   2.67e-02 1.78e+01
        pdb=" CG  TRP B 476 "    0.072 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 476 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 476 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 476 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 476 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 476 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 476 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 476 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 476 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 627 "   -0.060 5.00e-02 4.00e+02   9.29e-02 1.38e+01
        pdb=" N   PRO A 628 "    0.161 5.00e-02 4.00e+02
        pdb=" CA  PRO A 628 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A 628 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 321 "    0.010 2.00e-02 2.50e+03   2.00e-02 3.99e+00
        pdb=" C   ILE B 321 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ILE B 321 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PHE B 322 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1259 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 138
        2.66 -     3.22: 7319
        3.22 -     3.78: 11063
        3.78 -     4.34: 15376
        4.34 -     4.90: 25040
  Nonbonded interactions: 58936
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 446 "
            pdb=" OG  SER B 449 "
     model   vdw
     2.104 3.040
  nonbonded pdb=" OH  TYR B 111 "
            pdb=" OE2 GLU B 348 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" OH  TYR A 469 "
            pdb=" O   PRO A 488 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" O   TRP A 492 "
            pdb=" NZ  LYS A 511 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OG  SER B  75 "
            pdb=" O   ALA B 224 "
     model   vdw
     2.203 3.040
  ... (remaining 58931 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.460
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.240
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.182   7472  Z= 0.258
  Angle     :  0.894  27.903  10177  Z= 0.467
  Chirality :  0.048   0.461   1195
  Planarity :  0.005   0.093   1258
  Dihedral  : 13.768  89.228   2629
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 15.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.48 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 are not related in a simple way.
  whole: -2.67 (0.27), residues: 915
  helix: -1.08 (0.24), residues: 461
  sheet: -2.92 (0.63), residues: 63
  loop : -2.34 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 563 
 TYR   0.015   0.002   TYR A 629 
 PHE   0.023   0.002   PHE A 291 
 TRP   0.072   0.003   TRP B 476 
 HIS   0.011   0.001   HIS B 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00511 /  0.24 ( 7463)
  covalent geometry    : angle       0.81890 /  0.44 (10151)
  SS BOND              : bond        0.18201 /  9.58 (    1)
  SS BOND              : angle      22.52824 / 12.94 (    2)
  hydrogen bonds       : bond        0.19373 / 12.91 (  318)
  hydrogen bonds       : angle       7.61254 /  5.57 (  924)
  link_BETA1-4         : bond        0.00543 /  0.27 (    4)
  link_BETA1-4         : angle       2.27726 /  1.17 (   12)
  link_NAG-ASN         : bond        0.00269 /  0.14 (    4)
  link_NAG-ASN         : angle       4.59765 /  2.49 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: B  476 TRP cc_start: 0.3558 (m100) cc_final: 0.2302 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.0755
  time to fit residues: 16.9668
Evaluate side-chains
  125 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0270
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6838

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 235 GLN
B 110 HIS
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 285 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.154741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.138576 restraints weight = 11902.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.17
r_work: 0.3637 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3519 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7472  Z= 0.154
  Angle     :  0.731  11.792  10177  Z= 0.352
  Chirality :  0.045   0.303   1195
  Planarity :  0.005   0.055   1258
  Dihedral  :  5.450  22.183    983
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.38 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 are not related in a simple way.
  whole: -2.42 (0.27), residues: 915
  helix: -0.69 (0.23), residues: 486
  sheet: -2.77 (0.57), residues: 72
  loop : -2.57 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 148 
 TYR   0.028   0.002   TYR A 313 
 PHE   0.024   0.002   PHE A 524 
 TRP   0.023   0.002   TRP B 476 
 HIS   0.006   0.001   HIS B 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.15 ( 7463)
  covalent geometry    : angle       0.71652 /  0.35 (10151)
  SS BOND              : bond        0.00664 /  0.35 (    1)
  SS BOND              : angle       0.97301 /  0.57 (    2)
  hydrogen bonds       : bond        0.04499 /  3.05 (  318)
  hydrogen bonds       : angle       5.18754 /  3.77 (  924)
  link_BETA1-4         : bond        0.00412 /  0.21 (    4)
  link_BETA1-4         : angle       2.12300 /  1.06 (   12)
  link_NAG-ASN         : bond        0.00405 /  0.21 (    4)
  link_NAG-ASN         : angle       3.70661 /  2.02 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 0.284 
Fit side-chains
REVERT: B  382 SER cc_start: 0.8513 (p) cc_final: 0.8312 (t)
REVERT: B  476 TRP cc_start: 0.4640 (m100) cc_final: 0.3411 (m100)
  outliers start: 10
  outliers final: 5
  residues processed: 151
  average time/residue: 0.0709
  time to fit residues: 15.4971
Evaluate side-chains
  132 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 127
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  480 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 31 optimal weight:    0.1980
   chunk 83 optimal weight:    0.0040
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.7994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.154658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.138877 restraints weight = 11786.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.12
r_work: 0.3635 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3517 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7472  Z= 0.148
  Angle     :  0.684  10.804  10177  Z= 0.329
  Chirality :  0.044   0.287   1195
  Planarity :  0.004   0.049   1258
  Dihedral  :  5.187  21.027    983
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.60 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 are not related in a simple way.
  whole: -2.03 (0.27), residues: 915
  helix: -0.29 (0.24), residues: 480
  sheet: -2.61 (0.62), residues: 64
  loop : -2.51 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 563 
 TYR   0.029   0.001   TYR A 313 
 PHE   0.024   0.002   PHE A 524 
 TRP   0.017   0.001   TRP B 476 
 HIS   0.004   0.001   HIS B 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 ( 7463)
  covalent geometry    : angle       0.66983 /  0.33 (10151)
  SS BOND              : bond        0.00091 /  0.05 (    1)
  SS BOND              : angle       0.39754 /  0.23 (    2)
  hydrogen bonds       : bond        0.04021 /  2.74 (  318)
  hydrogen bonds       : angle       4.85781 /  3.50 (  924)
  link_BETA1-4         : bond        0.00487 /  0.24 (    4)
  link_BETA1-4         : angle       2.11397 /  1.06 (   12)
  link_NAG-ASN         : bond        0.00351 /  0.18 (    4)
  link_NAG-ASN         : angle       3.53374 /  1.91 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  186 LEU cc_start: 0.8092 (mm) cc_final: 0.7812 (mp)
REVERT: A  485 MET cc_start: 0.7112 (ppp) cc_final: 0.6159 (tpt)
REVERT: B  382 SER cc_start: 0.8555 (p) cc_final: 0.8308 (t)
REVERT: B  417 MET cc_start: 0.6121 (OUTLIER) cc_final: 0.5893 (ppp)
REVERT: B  476 TRP cc_start: 0.4621 (m100) cc_final: 0.3370 (m100)
REVERT: B  480 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6213 (ttm)
  outliers start: 17
  outliers final: 11
  residues processed: 151
  average time/residue: 0.0694
  time to fit residues: 15.4415
Evaluate side-chains
  134 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  417 MET
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  480 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 77 optimal weight:    0.4980
   chunk 47 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0970
   overall best weight:    0.6178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.161894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.145179 restraints weight = 12367.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 2.41
r_work: 0.3733 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7472  Z= 0.132
  Angle     :  0.656  10.955  10177  Z= 0.314
  Chirality :  0.043   0.270   1195
  Planarity :  0.004   0.053   1258
  Dihedral  :  5.018  22.076    983
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.14 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 are not related in a simple way.
  whole: -1.77 (0.28), residues: 915
  helix: -0.06 (0.24), residues: 475
  sheet: -2.37 (0.66), residues: 64
  loop : -2.40 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 535 
 TYR   0.021   0.001   TYR A 313 
 PHE   0.025   0.001   PHE A 524 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.002   0.001   HIS B 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 ( 7463)
  covalent geometry    : angle       0.64166 /  0.31 (10151)
  SS BOND              : bond        0.00088 /  0.05 (    1)
  SS BOND              : angle       0.31487 /  0.18 (    2)
  hydrogen bonds       : bond        0.03686 /  2.52 (  318)
  hydrogen bonds       : angle       4.62836 /  3.33 (  924)
  link_BETA1-4         : bond        0.00543 /  0.27 (    4)
  link_BETA1-4         : angle       2.10256 /  1.06 (   12)
  link_NAG-ASN         : bond        0.00385 /  0.19 (    4)
  link_NAG-ASN         : angle       3.45911 /  1.87 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  186 LEU cc_start: 0.7902 (mm) cc_final: 0.7656 (mp)
REVERT: A  262 LEU cc_start: 0.8160 (tp) cc_final: 0.7885 (tp)
REVERT: A  485 MET cc_start: 0.7005 (ppp) cc_final: 0.6093 (tpt)
REVERT: A  564 PHE cc_start: 0.8320 (m-80) cc_final: 0.7948 (m-80)
REVERT: B  315 PHE cc_start: 0.7551 (p90) cc_final: 0.7313 (p90)
REVERT: B  354 ILE cc_start: 0.8505 (mt) cc_final: 0.8299 (mm)
REVERT: B  382 SER cc_start: 0.8448 (p) cc_final: 0.8179 (t)
REVERT: B  417 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5844 (ppp)
REVERT: B  476 TRP cc_start: 0.4198 (m100) cc_final: 0.3117 (m100)
REVERT: B  480 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.6085 (ttm)
  outliers start: 21
  outliers final: 13
  residues processed: 148
  average time/residue: 0.0649
  time to fit residues: 14.4736
Evaluate side-chains
  144 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  417 MET
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  480 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 6 optimal weight:    0.0870
   chunk 76 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 11 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.6958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.155732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.139753 restraints weight = 11953.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.15
r_work: 0.3654 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3537 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   7472  Z= 0.135
  Angle     :  0.666  11.181  10177  Z= 0.317
  Chirality :  0.043   0.263   1195
  Planarity :  0.004   0.054   1258
  Dihedral  :  4.893  21.447    983
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 15.81 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 are not related in a simple way.
  whole: -1.60 (0.28), residues: 915
  helix:  0.06 (0.24), residues: 474
  sheet: -2.14 (0.71), residues: 64
  loop : -2.32 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 563 
 TYR   0.030   0.001   TYR A 313 
 PHE   0.026   0.001   PHE A 524 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.002   0.001   HIS B 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 ( 7463)
  covalent geometry    : angle       0.65246 /  0.31 (10151)
  SS BOND              : bond        0.00111 /  0.06 (    1)
  SS BOND              : angle       0.29054 /  0.16 (    2)
  hydrogen bonds       : bond        0.03585 /  2.46 (  318)
  hydrogen bonds       : angle       4.59115 /  3.30 (  924)
  link_BETA1-4         : bond        0.00541 /  0.27 (    4)
  link_BETA1-4         : angle       2.10735 /  1.06 (   12)
  link_NAG-ASN         : bond        0.00360 /  0.18 (    4)
  link_NAG-ASN         : angle       3.40038 /  1.82 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  485 MET cc_start: 0.7218 (ppp) cc_final: 0.6232 (tpt)
REVERT: B  315 PHE cc_start: 0.7772 (p90) cc_final: 0.7530 (p90)
REVERT: B  354 ILE cc_start: 0.8614 (mt) cc_final: 0.8406 (mm)
REVERT: B  382 SER cc_start: 0.8498 (p) cc_final: 0.8244 (t)
REVERT: B  417 MET cc_start: 0.5971 (OUTLIER) cc_final: 0.5744 (ppp)
REVERT: B  476 TRP cc_start: 0.4498 (m100) cc_final: 0.3231 (m100)
REVERT: B  480 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6238 (ttm)
  outliers start: 20
  outliers final: 15
  residues processed: 145
  average time/residue: 0.0596
  time to fit residues: 13.1534
Evaluate side-chains
  147 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  417 MET
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  480 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 3 optimal weight:    0.2980
   chunk 67 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 62 optimal weight:    0.1980
   chunk 80 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.156531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.140594 restraints weight = 11867.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 2.14
r_work: 0.3662 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3545 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7472  Z= 0.129
  Angle     :  0.652  11.600  10177  Z= 0.310
  Chirality :  0.043   0.260   1195
  Planarity :  0.004   0.054   1258
  Dihedral  :  4.807  22.420    983
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.10 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 are not related in a simple way.
  whole: -1.47 (0.28), residues: 915
  helix:  0.19 (0.24), residues: 473
  sheet: -2.18 (0.67), residues: 64
  loop : -2.27 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 535 
 TYR   0.031   0.001   TYR A 313 
 PHE   0.028   0.001   PHE A 524 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.004   0.001   HIS B 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 ( 7463)
  covalent geometry    : angle       0.63890 /  0.31 (10151)
  SS BOND              : bond        0.00123 /  0.06 (    1)
  SS BOND              : angle       0.28253 /  0.15 (    2)
  hydrogen bonds       : bond        0.03443 /  2.36 (  318)
  hydrogen bonds       : angle       4.49651 /  3.23 (  924)
  link_BETA1-4         : bond        0.00554 /  0.28 (    4)
  link_BETA1-4         : angle       2.10267 /  1.05 (   12)
  link_NAG-ASN         : bond        0.00354 /  0.18 (    4)
  link_NAG-ASN         : angle       3.34506 /  1.79 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A  485 MET cc_start: 0.7221 (ppp) cc_final: 0.6199 (tpt)
REVERT: B  315 PHE cc_start: 0.7768 (p90) cc_final: 0.7544 (p90)
REVERT: B  382 SER cc_start: 0.8479 (p) cc_final: 0.8229 (t)
REVERT: B  417 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5807 (ppp)
REVERT: B  476 TRP cc_start: 0.4462 (m100) cc_final: 0.3166 (m100)
REVERT: B  480 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6273 (ttm)
  outliers start: 22
  outliers final: 17
  residues processed: 150
  average time/residue: 0.0666
  time to fit residues: 14.9691
Evaluate side-chains
  153 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain B residue  163 LEU
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  417 MET
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  480 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0030
   chunk 28 optimal weight:    0.4980
   chunk 67 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 84 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0870
   chunk 48 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    0.4168

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.158200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.142309 restraints weight = 11862.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3761 rms_B_bonded: 2.17
r_work: 0.3682 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3564 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7472  Z= 0.121
  Angle     :  0.643  11.186  10177  Z= 0.309
  Chirality :  0.042   0.256   1195
  Planarity :  0.004   0.054   1258
  Dihedral  :  4.680  21.823    983
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.87 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 are not related in a simple way.
  whole: -1.31 (0.28), residues: 915
  helix:  0.29 (0.25), residues: 472
  sheet: -2.10 (0.66), residues: 64
  loop : -2.15 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 535 
 TYR   0.025   0.001   TYR A 313 
 PHE   0.028   0.001   PHE A 524 
 TRP   0.010   0.001   TRP B 128 
 HIS   0.002   0.001   HIS B 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 ( 7463)
  covalent geometry    : angle       0.62980 /  0.31 (10151)
  SS BOND              : bond        0.00108 /  0.06 (    1)
  SS BOND              : angle       0.24087 /  0.13 (    2)
  hydrogen bonds       : bond        0.03293 /  2.25 (  318)
  hydrogen bonds       : angle       4.36534 /  3.12 (  924)
  link_BETA1-4         : bond        0.00547 /  0.27 (    4)
  link_BETA1-4         : angle       2.11525 /  1.06 (   12)
  link_NAG-ASN         : bond        0.00375 /  0.19 (    4)
  link_NAG-ASN         : angle       3.30910 /  1.78 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  307 LEU cc_start: 0.8504 (tp) cc_final: 0.7971 (mt)
REVERT: A  485 MET cc_start: 0.7227 (ppp) cc_final: 0.6205 (tpt)
REVERT: B  315 PHE cc_start: 0.7755 (p90) cc_final: 0.7544 (p90)
REVERT: B  382 SER cc_start: 0.8573 (p) cc_final: 0.8339 (t)
REVERT: B  417 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5755 (ppp)
REVERT: B  476 TRP cc_start: 0.4257 (m100) cc_final: 0.3142 (m100)
REVERT: B  480 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6423 (ttm)
  outliers start: 21
  outliers final: 14
  residues processed: 155
  average time/residue: 0.0717
  time to fit residues: 16.2153
Evaluate side-chains
  151 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  417 MET
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  480 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 266 HIS
A 268 ASN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.157226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.141357 restraints weight = 11922.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 2.15
r_work: 0.3670 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3552 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7472  Z= 0.135
  Angle     :  0.662  11.916  10177  Z= 0.312
  Chirality :  0.043   0.263   1195
  Planarity :  0.004   0.052   1258
  Dihedral  :  4.715  22.470    983
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 17.99 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 are not related in a simple way.
  whole: -1.25 (0.28), residues: 915
  helix:  0.33 (0.25), residues: 473
  sheet: -2.07 (0.67), residues: 64
  loop : -2.11 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 563 
 TYR   0.029   0.001   TYR A 313 
 PHE   0.027   0.001   PHE A 524 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.002   0.001   HIS B 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.13 ( 7463)
  covalent geometry    : angle       0.64934 /  0.31 (10151)
  SS BOND              : bond        0.00146 /  0.08 (    1)
  SS BOND              : angle       0.25981 /  0.14 (    2)
  hydrogen bonds       : bond        0.03346 /  2.30 (  318)
  hydrogen bonds       : angle       4.36319 /  3.12 (  924)
  link_BETA1-4         : bond        0.00575 /  0.29 (    4)
  link_BETA1-4         : angle       2.09881 /  1.05 (   12)
  link_NAG-ASN         : bond        0.00330 /  0.17 (    4)
  link_NAG-ASN         : angle       3.26275 /  1.73 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A  290 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7270 (p0)
REVERT: A  485 MET cc_start: 0.7232 (ppp) cc_final: 0.6218 (tpt)
REVERT: B  315 PHE cc_start: 0.7748 (p90) cc_final: 0.7542 (p90)
REVERT: B  382 SER cc_start: 0.8515 (p) cc_final: 0.8256 (t)
REVERT: B  417 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5890 (ppp)
REVERT: B  476 TRP cc_start: 0.4336 (m100) cc_final: 0.3118 (m100)
REVERT: B  480 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6337 (ttm)
  outliers start: 25
  outliers final: 20
  residues processed: 143
  average time/residue: 0.0633
  time to fit residues: 13.6239
Evaluate side-chains
  150 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  417 MET
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  479 ILE
Chi-restraints excluded: chain B residue  480 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 78 optimal weight:    0.0470
   chunk 55 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 29 optimal weight:    0.2980
   chunk 53 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 69 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0870
   overall best weight:    0.3456

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.158757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.143039 restraints weight = 11853.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 2.13
r_work: 0.3695 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3577 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7472  Z= 0.114
  Angle     :  0.656  11.107  10177  Z= 0.308
  Chirality :  0.042   0.255   1195
  Planarity :  0.004   0.054   1258
  Dihedral  :  4.628  22.230    983
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 18.89 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 are not related in a simple way.
  whole: -1.11 (0.28), residues: 915
  helix:  0.44 (0.25), residues: 470
  sheet: -1.86 (0.68), residues: 64
  loop : -2.05 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 304 
 TYR   0.031   0.001   TYR A 313 
 PHE   0.026   0.001   PHE A 524 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.002   0.001   HIS B 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.11 ( 7463)
  covalent geometry    : angle       0.64284 /  0.31 (10151)
  SS BOND              : bond        0.00112 /  0.06 (    1)
  SS BOND              : angle       0.21952 /  0.12 (    2)
  hydrogen bonds       : bond        0.03178 /  2.18 (  318)
  hydrogen bonds       : angle       4.26695 /  3.05 (  924)
  link_BETA1-4         : bond        0.00577 /  0.29 (    4)
  link_BETA1-4         : angle       2.11445 /  1.06 (   12)
  link_NAG-ASN         : bond        0.00373 /  0.19 (    4)
  link_NAG-ASN         : angle       3.22644 /  1.73 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A  485 MET cc_start: 0.7220 (ppp) cc_final: 0.6242 (tpt)
REVERT: B  382 SER cc_start: 0.8536 (p) cc_final: 0.8296 (t)
REVERT: B  417 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5827 (ppp)
REVERT: B  476 TRP cc_start: 0.4213 (m100) cc_final: 0.3161 (m100)
REVERT: B  480 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6297 (ttm)
  outliers start: 22
  outliers final: 17
  residues processed: 150
  average time/residue: 0.0653
  time to fit residues: 14.7370
Evaluate side-chains
  148 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  417 MET
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  480 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0570
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 77 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0670
   overall best weight:    0.4836

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 275 GLN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.158366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.142582 restraints weight = 11829.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.14
r_work: 0.3686 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3569 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7472  Z= 0.120
  Angle     :  0.670  11.409  10177  Z= 0.313
  Chirality :  0.043   0.255   1195
  Planarity :  0.004   0.033   1258
  Dihedral  :  4.591  22.601    983
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 19.41 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 are not related in a simple way.
  whole: -1.02 (0.28), residues: 915
  helix:  0.49 (0.25), residues: 469
  sheet: -1.71 (0.69), residues: 64
  loop : -1.98 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 563 
 TYR   0.028   0.001   TYR A 313 
 PHE   0.029   0.001   PHE A 524 
 TRP   0.011   0.001   TRP A 219 
 HIS   0.003   0.001   HIS B 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.12 ( 7463)
  covalent geometry    : angle       0.65818 /  0.31 (10151)
  SS BOND              : bond        0.00124 /  0.07 (    1)
  SS BOND              : angle       0.20879 /  0.11 (    2)
  hydrogen bonds       : bond        0.03173 /  2.18 (  318)
  hydrogen bonds       : angle       4.25296 /  3.03 (  924)
  link_BETA1-4         : bond        0.00587 /  0.29 (    4)
  link_BETA1-4         : angle       2.10053 /  1.05 (   12)
  link_NAG-ASN         : bond        0.00355 /  0.18 (    4)
  link_NAG-ASN         : angle       3.21290 /  1.71 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  290 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7276 (p0)
REVERT: A  485 MET cc_start: 0.7251 (ppp) cc_final: 0.6259 (tpt)
REVERT: B  382 SER cc_start: 0.8568 (p) cc_final: 0.8313 (t)
REVERT: B  476 TRP cc_start: 0.4313 (m100) cc_final: 0.3222 (m100)
REVERT: B  480 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6346 (ttm)
  outliers start: 20
  outliers final: 15
  residues processed: 143
  average time/residue: 0.0621
  time to fit residues: 13.6859
Evaluate side-chains
  147 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  290 ASP
Chi-restraints excluded: chain A residue  322 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  331 MET
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  423 VAL
Chi-restraints excluded: chain B residue  465 TYR
Chi-restraints excluded: chain B residue  480 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 71 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0270
   chunk 53 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0040
   overall best weight:    0.4850

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 268 ASN
** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.158990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.143356 restraints weight = 11841.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.12
r_work: 0.3697 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3581 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7472  Z= 0.120
  Angle     :  0.671  11.432  10177  Z= 0.313
  Chirality :  0.042   0.255   1195
  Planarity :  0.004   0.033   1258
  Dihedral  :  4.585  22.296    983
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.41 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 are not related in a simple way.
  whole: -0.97 (0.28), residues: 915
  helix:  0.54 (0.25), residues: 469
  sheet: -1.63 (0.75), residues: 57
  loop : -2.00 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 563 
 TYR   0.025   0.001   TYR A 313 
 PHE   0.028   0.001   PHE A 524 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.002   0.001   HIS B 350 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.12 ( 7463)
  covalent geometry    : angle       0.65864 /  0.31 (10151)
  SS BOND              : bond        0.00120 /  0.06 (    1)
  SS BOND              : angle       0.19862 /  0.11 (    2)
  hydrogen bonds       : bond        0.03083 /  2.12 (  318)
  hydrogen bonds       : angle       4.23803 /  3.01 (  924)
  link_BETA1-4         : bond        0.00585 /  0.29 (    4)
  link_BETA1-4         : angle       2.09813 /  1.05 (   12)
  link_NAG-ASN         : bond        0.00355 /  0.18 (    4)
  link_NAG-ASN         : angle       3.18028 /  1.69 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2038.34 seconds
wall clock time: 35 minutes 49.58 seconds (2149.58 seconds total)