Starting phenix.real_space_refine
on Wed Mar 12 05:43:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p9v_13267/03_2025/7p9v_13267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p9v_13267/03_2025/7p9v_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p9v_13267/03_2025/7p9v_13267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p9v_13267/03_2025/7p9v_13267.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p9v_13267/03_2025/7p9v_13267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p9v_13267/03_2025/7p9v_13267.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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 dihedrals: 6
          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 dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "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 dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.82, per 1000 atoms: 0.66
  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: 1.80
  Conformation dependent library (CDL) restraints added in 921.6 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: 0.71
  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: 1.84

  Time building geometry restraints manager: 2.13 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 -    21.89: 4167
       21.89 -    43.78: 280
       43.78 -    65.66: 29
       65.66 -    87.55: 11
       87.55 -   109.44: 9
  Dihedral angle restraints: 4496
    sinusoidal: 1857
      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 4493 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:             2.440
  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:             0.020
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.100
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
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      :  0.005   0.056   7463  Z= 0.332
  Angle     :  0.819  10.988  10151  Z= 0.439
  Chirality :  0.048   0.461   1195
  Planarity :  0.005   0.093   1258
  Dihedral  : 15.249 109.438   2797
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (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
 TRP   0.072   0.003   TRP B 476 
 HIS   0.011   0.001   HIS B 350 
 PHE   0.023   0.002   PHE A 291 
 TYR   0.015   0.002   TYR A 629 
 ARG   0.005   0.001   ARG A 563 

*********************** 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  : 1.347 
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: 0.1868
  time to fit residues: 41.7855
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  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0980
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0980
   overall best weight:    0.4582

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

Flipped N/Q/H residues before XYZ refinement:
** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 HIS
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 285 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.155598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.139527 restraints weight = 11764.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.15
r_work: 0.3649 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3532 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7463  Z= 0.212
  Angle     :  0.710  11.276  10151  Z= 0.345
  Chirality :  0.045   0.328   1195
  Planarity :  0.005   0.058   1258
  Dihedral  : 10.885  89.472   1151
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.00 %
    Favored  : 89.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.27), residues: 915
  helix: -0.60 (0.23), residues: 482
  sheet: -2.57 (0.62), residues: 64
  loop : -2.60 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 476 
 HIS   0.006   0.001   HIS B 359 
 PHE   0.026   0.002   PHE A 524 
 TYR   0.027   0.002   TYR A 313 
 ARG   0.005   0.001   ARG B 148 

*********************** 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
  164 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 155
  time to evaluate  : 0.875 
Fit side-chains
REVERT: B  476 TRP cc_start: 0.4510 (m100) cc_final: 0.3339 (m100)
  outliers start: 9
  outliers final: 5
  residues processed: 157
  average time/residue: 0.1757
  time to fit residues: 39.3242
Evaluate side-chains
  133 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
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 16 optimal weight:    2.9990
   chunk 43 optimal weight:    0.1980
   chunk 0 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 47 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0570
   chunk 33 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.5902

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

Flipped N/Q/H residues before XYZ refinement:
A 235 GLN
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 217 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 = 0.3931 r_free = 0.3931 target = 0.156821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.141023 restraints weight = 11927.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 2.16
r_work: 0.3652 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3535 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7463  Z= 0.199
  Angle     :  0.673  10.277  10151  Z= 0.323
  Chirality :  0.044   0.306   1195
  Planarity :  0.004   0.052   1258
  Dihedral  :  9.734  75.031   1151
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.47 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.27), residues: 915
  helix: -0.20 (0.24), residues: 475
  sheet: -2.51 (0.63), residues: 64
  loop : -2.41 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 476 
 HIS   0.005   0.001   HIS B 359 
 PHE   0.025   0.002   PHE A 524 
 TYR   0.030   0.001   TYR A 313 
 ARG   0.003   0.000   ARG A 563 

*********************** 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
  165 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.769 
Fit side-chains
REVERT: A  186 LEU cc_start: 0.8078 (mm) cc_final: 0.7798 (mp)
REVERT: A  485 MET cc_start: 0.7167 (ppp) cc_final: 0.6156 (tpt)
REVERT: A  564 PHE cc_start: 0.8341 (m-80) cc_final: 0.8119 (m-80)
REVERT: B  417 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.4856 (ppp)
REVERT: B  476 TRP cc_start: 0.4540 (m100) cc_final: 0.3349 (m100)
REVERT: B  480 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.6167 (ttm)
  outliers start: 17
  outliers final: 10
  residues processed: 153
  average time/residue: 0.1470
  time to fit residues: 32.7231
Evaluate side-chains
  140 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
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  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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0370
   chunk 22 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0870
   chunk 46 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.4836

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

Flipped N/Q/H residues before XYZ refinement:
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 217 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 = 0.4061 r_free = 0.4061 target = 0.164094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.147501 restraints weight = 12307.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 2.41
r_work: 0.3767 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7463  Z= 0.181
  Angle     :  0.646  10.417  10151  Z= 0.309
  Chirality :  0.043   0.292   1195
  Planarity :  0.004   0.056   1258
  Dihedral  :  8.919  64.734   1151
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.14 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.28), residues: 915
  helix: -0.00 (0.24), residues: 475
  sheet: -2.23 (0.67), residues: 64
  loop : -2.33 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 476 
 HIS   0.003   0.000   HIS B 359 
 PHE   0.025   0.001   PHE A 524 
 TYR   0.029   0.001   TYR A 313 
 ARG   0.004   0.000   ARG A 563 

*********************** 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
  159 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.795 
Fit side-chains
REVERT: A  186 LEU cc_start: 0.7916 (mm) cc_final: 0.7664 (mp)
REVERT: A  485 MET cc_start: 0.6943 (ppp) cc_final: 0.6064 (tpt)
REVERT: B  417 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5616 (ppp)
REVERT: B  476 TRP cc_start: 0.4077 (m100) cc_final: 0.3056 (m100)
REVERT: B  480 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.6085 (ttm)
  outliers start: 20
  outliers final: 12
  residues processed: 147
  average time/residue: 0.1368
  time to fit residues: 29.8867
Evaluate side-chains
  146 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
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  283 LEU
Chi-restraints excluded: chain B residue  299 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0000
   chunk 16 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   chunk 89 optimal weight:    0.0980
   chunk 37 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.158162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.141698 restraints weight = 11788.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 2.25
r_work: 0.3664 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3544 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7463  Z= 0.183
  Angle     :  0.651  10.670  10151  Z= 0.310
  Chirality :  0.043   0.284   1195
  Planarity :  0.004   0.055   1258
  Dihedral  :  8.208  57.180   1151
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.94 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.28), residues: 915
  helix:  0.13 (0.24), residues: 474
  sheet: -2.05 (0.70), residues: 64
  loop : -2.24 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 128 
 HIS   0.003   0.001   HIS B 350 
 PHE   0.026   0.001   PHE A 524 
 TYR   0.028   0.001   TYR A 313 
 ARG   0.004   0.000   ARG A 563 

*********************** 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
  160 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 1.060 
Fit side-chains
REVERT: A  485 MET cc_start: 0.7204 (ppp) cc_final: 0.6155 (tpt)
REVERT: B  315 PHE cc_start: 0.7769 (p90) cc_final: 0.7535 (p90)
REVERT: B  417 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.5676 (ppp)
REVERT: B  476 TRP cc_start: 0.4426 (m100) cc_final: 0.3218 (m100)
REVERT: B  480 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.6283 (ttm)
  outliers start: 18
  outliers final: 12
  residues processed: 150
  average time/residue: 0.1535
  time to fit residues: 33.2938
Evaluate side-chains
  147 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
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  281 ILE
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  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  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 26 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0470
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.8882

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

Flipped N/Q/H residues before XYZ refinement:
** B 217 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 = 0.3926 r_free = 0.3926 target = 0.156298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.140293 restraints weight = 11825.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 2.14
r_work: 0.3652 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3534 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7463  Z= 0.223
  Angle     :  0.665  11.779  10151  Z= 0.319
  Chirality :  0.044   0.280   1195
  Planarity :  0.004   0.052   1258
  Dihedral  :  7.683  56.707   1151
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 17.10 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.28), residues: 915
  helix:  0.17 (0.24), residues: 473
  sheet: -2.16 (0.67), residues: 64
  loop : -2.24 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 128 
 HIS   0.002   0.001   HIS B 359 
 PHE   0.027   0.001   PHE A 524 
 TYR   0.029   0.001   TYR A 313 
 ARG   0.004   0.000   ARG A 535 

*********************** 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: 24
    poor density    : 140
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A  485 MET cc_start: 0.7185 (ppp) cc_final: 0.6174 (tpt)
REVERT: B  315 PHE cc_start: 0.7736 (p90) cc_final: 0.7502 (p90)
REVERT: B  417 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5683 (ppp)
REVERT: B  476 TRP cc_start: 0.4530 (m100) cc_final: 0.3210 (m100)
REVERT: B  480 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6291 (ttm)
  outliers start: 24
  outliers final: 15
  residues processed: 149
  average time/residue: 0.1400
  time to fit residues: 30.8932
Evaluate side-chains
  151 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
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  451 LEU
Chi-restraints excluded: chain B residue  195 THR
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  417 MET
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 73 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 83 optimal weight:    0.3980
   chunk 58 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 15 optimal weight:    7.9990
   chunk 75 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 217 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 = 0.3940 r_free = 0.3940 target = 0.157436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.141372 restraints weight = 11708.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.15
r_work: 0.3675 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3555 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7463  Z= 0.192
  Angle     :  0.652  11.270  10151  Z= 0.313
  Chirality :  0.043   0.270   1195
  Planarity :  0.004   0.053   1258
  Dihedral  :  7.262  55.334   1151
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 17.35 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.28), residues: 915
  helix:  0.27 (0.24), residues: 471
  sheet: -2.09 (0.67), residues: 64
  loop : -2.16 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 128 
 HIS   0.003   0.001   HIS B 350 
 PHE   0.028   0.001   PHE A 524 
 TYR   0.025   0.001   TYR A 313 
 ARG   0.004   0.000   ARG A 563 

*********************** 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
  170 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.720 
Fit side-chains
REVERT: A  291 PHE cc_start: 0.7678 (t80) cc_final: 0.7452 (t80)
REVERT: A  485 MET cc_start: 0.7202 (ppp) cc_final: 0.6192 (tpt)
REVERT: B  315 PHE cc_start: 0.7757 (p90) cc_final: 0.7536 (p90)
REVERT: B  417 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5883 (ppp)
REVERT: B  476 TRP cc_start: 0.4265 (m100) cc_final: 0.2990 (m100)
REVERT: B  480 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6273 (ttm)
  outliers start: 24
  outliers final: 17
  residues processed: 155
  average time/residue: 0.1414
  time to fit residues: 32.2143
Evaluate side-chains
  155 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
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 A residue  627 PHE
Chi-restraints excluded: chain B residue  195 THR
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  338 VAL
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  479 ILE
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 90 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0770
   chunk 7 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.9142

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

Flipped N/Q/H residues before XYZ refinement:
A 266 HIS
A 268 ASN
** B 217 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 = 0.3923 r_free = 0.3923 target = 0.156093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.139979 restraints weight = 11867.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.16
r_work: 0.3650 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3533 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7463  Z= 0.228
  Angle     :  0.684  11.953  10151  Z= 0.325
  Chirality :  0.044   0.268   1195
  Planarity :  0.004   0.050   1258
  Dihedral  :  7.037  56.085   1151
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 18.77 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.28), residues: 915
  helix:  0.30 (0.24), residues: 471
  sheet: -2.16 (0.66), residues: 64
  loop : -2.14 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 128 
 HIS   0.003   0.001   HIS B 418 
 PHE   0.027   0.001   PHE A 524 
 TYR   0.030   0.001   TYR A 313 
 ARG   0.003   0.000   ARG A 563 

*********************** 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
  150 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.838 
Fit side-chains
REVERT: A  485 MET cc_start: 0.7221 (ppp) cc_final: 0.6237 (tpt)
REVERT: B  315 PHE cc_start: 0.7764 (p90) cc_final: 0.7542 (p90)
REVERT: B  476 TRP cc_start: 0.4425 (m100) cc_final: 0.3097 (m100)
REVERT: B  480 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6313 (ttm)
  outliers start: 21
  outliers final: 19
  residues processed: 139
  average time/residue: 0.1421
  time to fit residues: 29.0669
Evaluate side-chains
  147 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
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  627 PHE
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  195 THR
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  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 42 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0470
   chunk 40 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
** B 217 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 = 0.3934 r_free = 0.3934 target = 0.156995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.140826 restraints weight = 11931.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 2.18
r_work: 0.3662 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3544 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7463  Z= 0.199
  Angle     :  0.691  11.620  10151  Z= 0.325
  Chirality :  0.043   0.262   1195
  Planarity :  0.004   0.051   1258
  Dihedral  :  6.803  55.567   1151
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 18.51 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.28), residues: 915
  helix:  0.35 (0.24), residues: 471
  sheet: -2.16 (0.66), residues: 64
  loop : -2.09 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 128 
 HIS   0.002   0.001   HIS B 373 
 PHE   0.026   0.001   PHE A 524 
 TYR   0.032   0.001   TYR A 313 
 ARG   0.003   0.000   ARG B 148 

*********************** 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
  158 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A  485 MET cc_start: 0.7315 (ppp) cc_final: 0.6301 (tpt)
REVERT: A  564 PHE cc_start: 0.7742 (m-80) cc_final: 0.7307 (m-80)
REVERT: B  315 PHE cc_start: 0.7756 (p90) cc_final: 0.7538 (p90)
REVERT: B  476 TRP cc_start: 0.4340 (m100) cc_final: 0.3146 (m100)
REVERT: B  480 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6290 (ttm)
  outliers start: 25
  outliers final: 20
  residues processed: 144
  average time/residue: 0.1417
  time to fit residues: 30.1520
Evaluate side-chains
  147 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
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  451 LEU
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  195 THR
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  351 LEU
Chi-restraints excluded: chain B residue  392 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 24 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9980
   chunk 85 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** B 217 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 = 0.3931 r_free = 0.3931 target = 0.156694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.140456 restraints weight = 12024.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 2.20
r_work: 0.3658 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3541 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7463  Z= 0.214
  Angle     :  0.696  11.724  10151  Z= 0.328
  Chirality :  0.044   0.258   1195
  Planarity :  0.004   0.050   1258
  Dihedral  :  6.598  55.827   1151
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.54 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.28), residues: 915
  helix:  0.35 (0.24), residues: 470
  sheet: -2.09 (0.68), residues: 64
  loop : -2.04 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 128 
 HIS   0.002   0.001   HIS B 359 
 PHE   0.029   0.002   PHE A 524 
 TYR   0.030   0.001   TYR A 313 
 ARG   0.003   0.000   ARG A 563 

********************** 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
  155 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.728 
Fit side-chains
REVERT: A  485 MET cc_start: 0.7359 (ppp) cc_final: 0.6316 (tpt)
REVERT: B  315 PHE cc_start: 0.7759 (p90) cc_final: 0.7540 (p90)
REVERT: B  476 TRP cc_start: 0.4513 (m100) cc_final: 0.3208 (m100)
REVERT: B  480 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6295 (ttm)
  outliers start: 22
  outliers final: 19
  residues processed: 144
  average time/residue: 0.1309
  time to fit residues: 28.4531
Evaluate side-chains
  145 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
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  445 PHE
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  195 THR
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  351 LEU
Chi-restraints excluded: chain B residue  392 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 28 optimal weight:    0.1980
   chunk 36 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0670
   chunk 21 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0010
   chunk 43 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.3724

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

Flipped N/Q/H residues before XYZ refinement:
A 268 ASN
** B 217 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 = 0.3957 r_free = 0.3957 target = 0.158991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.143045 restraints weight = 11820.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.14
r_work: 0.3691 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3573 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7463  Z= 0.175
  Angle     :  0.675  11.013  10151  Z= 0.316
  Chirality :  0.043   0.251   1195
  Planarity :  0.004   0.052   1258
  Dihedral  :  6.395  54.547   1151
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 19.79 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.28), residues: 915
  helix:  0.48 (0.25), residues: 470
  sheet: -1.89 (0.70), residues: 64
  loop : -2.03 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 128 
 HIS   0.002   0.001   HIS B 350 
 PHE   0.029   0.001   PHE A 524 
 TYR   0.028   0.001   TYR A 313 
 ARG   0.003   0.000   ARG B 148 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4132.68 seconds
wall clock time: 73 minutes 4.16 seconds (4384.16 seconds total)