Starting phenix.real_space_refine
on Thu Mar 13 18:17:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yvu_34138/03_2025/7yvu_34138.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yvu_34138/03_2025/7yvu_34138.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yvu_34138/03_2025/7yvu_34138.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yvu_34138/03_2025/7yvu_34138.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yvu_34138/03_2025/7yvu_34138.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yvu_34138/03_2025/7yvu_34138.cif"
  }
  resolution = 3.2
  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=   0.001 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3164 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4124      2.51       5
     N    1081      2.21       5
     O    1213      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6456
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4856
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1557
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 12, 'TRANS': 182}
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' ZN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.61, per 1000 atoms: 0.87
  Number of scatterers: 6456
  At special positions: 0
  Unit cell: (81.07, 90.45, 114.57, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     O    1213      8.00
     N    1081      7.00
     C    4124      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A  53 "
      " NAG A 702 " - " ASN A 546 "
      " NAG B 601 " - " ASN B 343 "
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 842.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 703 "
        pdb="ZN    ZN A 703 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 703 " - pdb=" NE2 HIS A 378 "


  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 4 sheets defined
      57.3% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 52
      removed outlier: 4.352A  pdb=" N   ASN A  24 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ASP A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   SER A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.571A  pdb=" N   GLN A  60 " --> pdb=" O   GLU A  56 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS A  68 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   TRP A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
    Processing helix  chain 'A' and resid 90 through 102
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 147 through 155
      removed outlier: 3.597A  pdb=" N   SER A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.842A  pdb=" N   ALA A 164 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   LYS A 174 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.741A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 221 through 232
      removed outlier: 3.713A  pdb=" N   GLU A 232 " --> pdb=" O   ARG A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 3.656A  pdb=" N   HIS A 239 " --> pdb=" O   PRO A 235 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ASP A 250 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 256
      removed outlier: 4.397A  pdb=" N   ILE A 256 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 253 through 256'
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 283
      Proline residue:  A 280  - end of helix
      removed outlier: 4.109A  pdb=" N   VAL A 283 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 301
    Processing helix  chain 'A' and resid 303 through 317
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.580A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.591A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 411
      removed outlier: 3.521A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.839A  pdb=" N   ILE A 436 " --> pdb=" O   SER A 432 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 472 through 478
    Processing helix  chain 'A' and resid 498 through 502
      removed outlier: 3.549A  pdb=" N   ALA A 501 " --> pdb=" O   CYS A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 508
      removed outlier: 3.571A  pdb=" N   ASN A 508 " --> pdb=" O   PHE A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.594A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ILE A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 4.078A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLN A 552 " --> pdb=" O   THR A 548 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LYS A 553 " --> pdb=" O   GLU A 549 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.810A  pdb=" N   ALA A 569 " --> pdb=" O   PRO A 565 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU A 570 " --> pdb=" O   TRP A 566 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLU A 571 " --> pdb=" O   THR A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.608A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 3.629A  pdb=" N   TYR B 369 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASN B 370 " --> pdb=" O   VAL B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 390
      removed outlier: 3.711A  pdb=" N   LEU B 390 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 4.041A  pdb=" N   SER B 408 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.681A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.277A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.059A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.774A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLY B 431 " --> pdb=" O   TYR B 380 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL B 433 " --> pdb=" O   LYS B 378 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LYS B 378 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454

    284 hydrogen bonds defined for protein.
    792 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: 1.68

  Time building geometry restraints manager: 1.75 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2080
        1.35 -     1.48: 1820
        1.48 -     1.61: 2680
        1.61 -     1.73: 0
        1.73 -     1.86: 58
  Bond restraints: 6638
  Sorted by residual:
  bond pdb=" CA  ASN A  49 "
       pdb=" C   ASN A  49 "
    ideal  model  delta    sigma   weight residual
    1.523  1.484  0.039 1.35e-02 5.49e+03 8.43e+00
  bond pdb=" N   GLU A 402 "
       pdb=" CA  GLU A 402 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.026 1.19e-02 7.06e+03 4.96e+00
  bond pdb=" CB  PRO B 521 "
       pdb=" CG  PRO B 521 "
    ideal  model  delta    sigma   weight residual
    1.492  1.570 -0.078 5.00e-02 4.00e+02 2.41e+00
  bond pdb=" CB  CYS B 379 "
       pdb=" SG  CYS B 379 "
    ideal  model  delta    sigma   weight residual
    1.808  1.859 -0.051 3.30e-02 9.18e+02 2.36e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.27e+00
  ... (remaining 6633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 8831
        1.97 -     3.94: 158
        3.94 -     5.91: 23
        5.91 -     7.88: 5
        7.88 -     9.84: 1
  Bond angle restraints: 9018
  Sorted by residual:
  angle pdb=" N   ILE B 468 "
        pdb=" CA  ILE B 468 "
        pdb=" C   ILE B 468 "
      ideal   model   delta    sigma   weight residual
     113.20  108.38    4.82 9.60e-01 1.09e+00 2.52e+01
  angle pdb=" C   ASP A 509 "
        pdb=" CA  ASP A 509 "
        pdb=" CB  ASP A 509 "
      ideal   model   delta    sigma   weight residual
     116.34  110.19    6.15 1.40e+00 5.10e-01 1.93e+01
  angle pdb=" C   LEU A 144 "
        pdb=" N   GLU A 145 "
        pdb=" CA  GLU A 145 "
      ideal   model   delta    sigma   weight residual
     121.80  131.64   -9.84 2.44e+00 1.68e-01 1.63e+01
  angle pdb=" N   CYS B 432 "
        pdb=" CA  CYS B 432 "
        pdb=" C   CYS B 432 "
      ideal   model   delta    sigma   weight residual
     108.14  114.18   -6.04 1.52e+00 4.33e-01 1.58e+01
  angle pdb=" CA  CYS B 432 "
        pdb=" CB  CYS B 432 "
        pdb=" SG  CYS B 432 "
      ideal   model   delta    sigma   weight residual
     114.40  121.85   -7.45 2.30e+00 1.89e-01 1.05e+01
  ... (remaining 9013 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.49: 3518
       17.49 -    34.98: 355
       34.98 -    52.46: 66
       52.46 -    69.95: 16
       69.95 -    87.44: 10
  Dihedral angle restraints: 3965
    sinusoidal: 1640
      harmonic: 2325
  Sorted by residual:
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  152.96  -59.96     1      1.00e+01 1.00e-02 4.79e+01
  dihedral pdb=" CB  CYS B 379 "
           pdb=" SG  CYS B 379 "
           pdb=" SG  CYS B 432 "
           pdb=" CB  CYS B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   42.17   50.83     1      1.00e+01 1.00e-02 3.54e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  129.29  -36.29     1      1.00e+01 1.00e-02 1.86e+01
  ... (remaining 3962 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 609
       0.037 -    0.073: 235
       0.073 -    0.110: 73
       0.110 -    0.147: 23
       0.147 -    0.183: 3
  Chirality restraints: 943
  Sorted by residual:
  chirality pdb=" CA  PRO B 521 "
            pdb=" N   PRO B 521 "
            pdb=" C   PRO B 521 "
            pdb=" CB  PRO B 521 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 8.40e-01
  chirality pdb=" C2  NAG A 701 "
            pdb=" C1  NAG A 701 "
            pdb=" C3  NAG A 701 "
            pdb=" N2  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.32   -0.17 2.00e-01 2.50e+01 7.50e-01
  chirality pdb=" CA  CYS B 432 "
            pdb=" N   CYS B 432 "
            pdb=" C   CYS B 432 "
            pdb=" CB  CYS B 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.27e-01
  ... (remaining 940 not shown)

  Planarity restraints: 1172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 520 "    0.078 5.00e-02 4.00e+02   1.17e-01 2.19e+01
        pdb=" N   PRO B 521 "   -0.202 5.00e-02 4.00e+02
        pdb=" CA  PRO B 521 "    0.064 5.00e-02 4.00e+02
        pdb=" CD  PRO B 521 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 145 "    0.070 5.00e-02 4.00e+02   1.06e-01 1.78e+01
        pdb=" N   PRO A 146 "   -0.183 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 252 "    0.038 5.00e-02 4.00e+02   5.86e-02 5.50e+00
        pdb=" N   PRO A 253 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 253 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 253 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1169 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 77
        2.66 -     3.22: 6007
        3.22 -     3.78: 9260
        3.78 -     4.34: 12549
        4.34 -     4.90: 21450
  Nonbonded interactions: 49343
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 402 "
            pdb="ZN    ZN A 703 "
     model   vdw
     2.103 2.230
  nonbonded pdb=" O   PHE A 327 "
            pdb=" OG  SER A 331 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" NH1 ARG B 457 "
            pdb=" OD2 ASP B 467 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" NH1 ARG A 177 "
            pdb=" O   GLU A 495 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" O   PRO B 384 "
            pdb=" OG1 THR B 385 "
     model   vdw
     2.292 3.040
  ... (remaining 49338 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.360
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   6638  Z= 0.266
  Angle     :  0.636   9.844   9018  Z= 0.341
  Chirality :  0.045   0.183    943
  Planarity :  0.007   0.117   1169
  Dihedral  : 14.813  87.438   2452
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  5.46 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.44 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.30), residues: 787
  helix:  0.61 (0.28), residues: 388
  sheet:  0.04 (0.71), residues: 50
  loop : -1.64 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 594 
 HIS   0.006   0.001   HIS A 378 
 PHE   0.023   0.001   PHE A 308 
 TYR   0.017   0.001   TYR A 381 
 ARG   0.006   0.000   ARG A 246 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 205
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.8354 (tptm) cc_final: 0.8014 (tptm)
REVERT: A  216 ASN cc_start: 0.7667 (m-40) cc_final: 0.7430 (m-40)
REVERT: A  402 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6352 (mm-30)
REVERT: A  421 ILE cc_start: 0.8013 (tp) cc_final: 0.7812 (tp)
REVERT: A  455 MET cc_start: 0.7398 (tmm) cc_final: 0.6952 (tmm)
REVERT: A  479 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7153 (tm-30)
REVERT: A  508 ASN cc_start: 0.7589 (m-40) cc_final: 0.7296 (t0)
REVERT: B  357 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7901 (ttp80)
REVERT: B  438 SER cc_start: 0.7762 (t) cc_final: 0.7441 (t)
REVERT: B  443 SER cc_start: 0.8240 (m) cc_final: 0.7986 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1816
  time to fit residues: 49.1792
Evaluate side-chains
  191 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 190
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.3980
   chunk 61 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
A 374 HIS
A 601 ASN
B 394 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.115678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.103612 restraints weight = 9693.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.15
r_work: 0.3184 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077   6638  Z= 0.310
  Angle     :  0.635  10.257   9018  Z= 0.323
  Chirality :  0.047   0.258    943
  Planarity :  0.007   0.118   1169
  Dihedral  :  6.261  59.379    932
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  5.84 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.77 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.30), residues: 787
  helix:  0.85 (0.27), residues: 391
  sheet: -0.21 (0.67), residues: 53
  loop : -1.53 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 477 
 HIS   0.006   0.001   HIS A 378 
 PHE   0.013   0.001   PHE A 308 
 TYR   0.021   0.001   TYR A 385 
 ARG   0.004   0.000   ARG A 465 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 191
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 ILE cc_start: 0.7992 (mt) cc_final: 0.7768 (tt)
REVERT: A   75 GLU cc_start: 0.8448 (tp30) cc_final: 0.8149 (tp30)
REVERT: A   78 LYS cc_start: 0.8615 (tptm) cc_final: 0.8279 (tptm)
REVERT: A   84 SER cc_start: 0.8665 (t) cc_final: 0.8451 (m)
REVERT: A   87 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7087 (tm-30)
REVERT: A  111 ASP cc_start: 0.8280 (m-30) cc_final: 0.8034 (t70)
REVERT: A  149 ASP cc_start: 0.8080 (t70) cc_final: 0.7862 (t70)
REVERT: A  421 ILE cc_start: 0.8750 (tp) cc_final: 0.8514 (tp)
REVERT: A  455 MET cc_start: 0.8469 (tmm) cc_final: 0.8091 (tmm)
REVERT: A  470 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8522 (tttp)
REVERT: A  479 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7974 (tm-30)
REVERT: A  508 ASN cc_start: 0.8122 (m-40) cc_final: 0.7659 (t0)
REVERT: A  556 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8274 (mtpp)
REVERT: B  438 SER cc_start: 0.8077 (t) cc_final: 0.7829 (t)
REVERT: B  443 SER cc_start: 0.8507 (m) cc_final: 0.8268 (m)
  outliers start: 12
  outliers final: 8
  residues processed: 195
  average time/residue: 0.1723
  time to fit residues: 44.4298
Evaluate side-chains
  198 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 189
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  394 ASN
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    0.0170
   chunk 68 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0670
   chunk 18 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
A 601 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.116688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.104581 restraints weight = 9756.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.16
r_work: 0.3197 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
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   0.080   6638  Z= 0.241
  Angle     :  0.596  10.328   9018  Z= 0.300
  Chirality :  0.044   0.264    943
  Planarity :  0.006   0.118   1169
  Dihedral  :  5.885  59.447    929
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  5.08 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.97 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.30), residues: 787
  helix:  0.89 (0.27), residues: 391
  sheet: -0.15 (0.65), residues: 53
  loop : -1.48 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.011   0.001   PHE A 308 
 TYR   0.018   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 465 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 185
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 ILE cc_start: 0.7929 (mt) cc_final: 0.7715 (tt)
REVERT: A   75 GLU cc_start: 0.8442 (tp30) cc_final: 0.8161 (tp30)
REVERT: A   78 LYS cc_start: 0.8615 (tptm) cc_final: 0.8278 (tptm)
REVERT: A   84 SER cc_start: 0.8572 (t) cc_final: 0.8264 (m)
REVERT: A   87 GLU cc_start: 0.7393 (tm-30) cc_final: 0.7063 (tm-30)
REVERT: A  111 ASP cc_start: 0.8323 (m-30) cc_final: 0.8060 (t70)
REVERT: A  149 ASP cc_start: 0.8086 (t70) cc_final: 0.7872 (t70)
REVERT: A  287 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8034 (mm-40)
REVERT: A  421 ILE cc_start: 0.8693 (tp) cc_final: 0.8435 (tp)
REVERT: A  455 MET cc_start: 0.8459 (tmm) cc_final: 0.8096 (tmm)
REVERT: A  470 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8462 (tttp)
REVERT: A  471 GLU cc_start: 0.7701 (pm20) cc_final: 0.7467 (pm20)
REVERT: A  479 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7958 (tm-30)
REVERT: A  508 ASN cc_start: 0.8056 (m-40) cc_final: 0.7650 (t0)
REVERT: A  556 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8248 (mtpp)
REVERT: B  347 PHE cc_start: 0.8412 (m-10) cc_final: 0.8117 (m-10)
REVERT: B  438 SER cc_start: 0.8103 (t) cc_final: 0.7846 (t)
REVERT: B  443 SER cc_start: 0.8505 (m) cc_final: 0.8264 (m)
  outliers start: 12
  outliers final: 6
  residues processed: 191
  average time/residue: 0.1813
  time to fit residues: 45.4196
Evaluate side-chains
  188 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 181
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0870
   chunk 21 optimal weight:    0.2980
   chunk 73 optimal weight:    0.0010
   chunk 15 optimal weight:    0.5980
   chunk 11 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.3164

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
A 601 ASN
B 394 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.118006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.105613 restraints weight = 9925.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.23
r_work: 0.3212 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   6638  Z= 0.199
  Angle     :  0.572  10.375   9018  Z= 0.286
  Chirality :  0.043   0.259    943
  Planarity :  0.006   0.117   1169
  Dihedral  :  5.754  59.093    929
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  4.96 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.87 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.30), residues: 787
  helix:  1.07 (0.27), residues: 385
  sheet:  0.27 (0.67), residues: 50
  loop : -1.55 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.009   0.001   PHE A 308 
 TYR   0.017   0.001   TYR A 535 
 ARG   0.003   0.000   ARG A 246 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 174
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8456 (tp30) cc_final: 0.8168 (tp30)
REVERT: A   78 LYS cc_start: 0.8575 (tptm) cc_final: 0.8227 (tptm)
REVERT: A   84 SER cc_start: 0.8531 (t) cc_final: 0.8279 (m)
REVERT: A  111 ASP cc_start: 0.8349 (m-30) cc_final: 0.8057 (t70)
REVERT: A  287 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8054 (mm-40)
REVERT: A  455 MET cc_start: 0.8470 (tmm) cc_final: 0.8121 (tmm)
REVERT: A  470 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8451 (tttp)
REVERT: A  479 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7928 (tm-30)
REVERT: A  508 ASN cc_start: 0.8018 (m-40) cc_final: 0.7662 (t0)
REVERT: A  556 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8246 (mtpp)
REVERT: B  347 PHE cc_start: 0.8438 (m-10) cc_final: 0.8111 (m-10)
REVERT: B  438 SER cc_start: 0.8135 (t) cc_final: 0.7840 (t)
REVERT: B  443 SER cc_start: 0.8450 (m) cc_final: 0.8198 (m)
  outliers start: 10
  outliers final: 4
  residues processed: 181
  average time/residue: 0.1657
  time to fit residues: 40.4428
Evaluate side-chains
  181 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 176
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  574 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0980
   chunk 5 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 61 optimal weight:    0.2980
   chunk 47 optimal weight:    0.3980
   chunk 57 optimal weight:    0.5980
   chunk 50 optimal weight:    0.3980
   overall best weight:    0.2578

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
A 601 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.118660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.106230 restraints weight = 9905.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 2.23
r_work: 0.3226 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   6638  Z= 0.185
  Angle     :  0.584  10.377   9018  Z= 0.291
  Chirality :  0.043   0.264    943
  Planarity :  0.006   0.117   1169
  Dihedral  :  5.660  58.590    929
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  4.45 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 17.47 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.30), residues: 787
  helix:  1.14 (0.27), residues: 385
  sheet:  0.09 (0.67), residues: 53
  loop : -1.45 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 436 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.009   0.001   PHE A 308 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 246 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 179
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8448 (tp30) cc_final: 0.8163 (tp30)
REVERT: A   78 LYS cc_start: 0.8565 (tptm) cc_final: 0.8233 (tptm)
REVERT: A   84 SER cc_start: 0.8502 (t) cc_final: 0.8295 (m)
REVERT: A  111 ASP cc_start: 0.8302 (m-30) cc_final: 0.8053 (t70)
REVERT: A  114 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7770 (mmtt)
REVERT: A  270 MET cc_start: 0.8825 (tpt) cc_final: 0.8354 (tpt)
REVERT: A  455 MET cc_start: 0.8449 (tmm) cc_final: 0.8105 (tmm)
REVERT: A  470 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8450 (tttp)
REVERT: A  479 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7892 (tm-30)
REVERT: A  489 GLU cc_start: 0.7911 (pm20) cc_final: 0.7696 (pm20)
REVERT: A  508 ASN cc_start: 0.8029 (m-40) cc_final: 0.7695 (t0)
REVERT: A  556 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8276 (mtpp)
REVERT: B  438 SER cc_start: 0.8106 (t) cc_final: 0.7867 (t)
REVERT: B  443 SER cc_start: 0.8417 (m) cc_final: 0.8165 (m)
  outliers start: 11
  outliers final: 7
  residues processed: 185
  average time/residue: 0.1770
  time to fit residues: 43.3992
Evaluate side-chains
  196 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 188
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  362 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 48 optimal weight:    0.3980
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0050
   chunk 19 optimal weight:    0.0020
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0050
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.2016

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
A 601 ASN
B 394 ASN
B 422 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.119747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.107450 restraints weight = 9678.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.16
r_work: 0.3253 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.082   6638  Z= 0.175
  Angle     :  0.570  10.359   9018  Z= 0.283
  Chirality :  0.042   0.258    943
  Planarity :  0.006   0.116   1169
  Dihedral  :  5.593  58.552    929
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  4.83 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.90 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.30), residues: 787
  helix:  1.23 (0.27), residues: 384
  sheet:  0.43 (0.69), residues: 50
  loop : -1.47 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.008   0.001   PHE A 308 
 TYR   0.017   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 246 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 184
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8468 (tp30) cc_final: 0.8202 (tp30)
REVERT: A   78 LYS cc_start: 0.8558 (tptm) cc_final: 0.8253 (tptm)
REVERT: A  114 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7765 (mmtt)
REVERT: A  270 MET cc_start: 0.8798 (tpt) cc_final: 0.8522 (tpt)
REVERT: A  287 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8105 (mm-40)
REVERT: A  402 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7169 (mm-30)
REVERT: A  455 MET cc_start: 0.8352 (tmm) cc_final: 0.8001 (tmm)
REVERT: A  470 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8470 (tttp)
REVERT: A  479 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: A  489 GLU cc_start: 0.7881 (pm20) cc_final: 0.7659 (pm20)
REVERT: A  508 ASN cc_start: 0.7962 (m-40) cc_final: 0.7756 (t0)
REVERT: A  556 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8285 (mtpp)
REVERT: B  438 SER cc_start: 0.8052 (t) cc_final: 0.7799 (t)
REVERT: B  443 SER cc_start: 0.8394 (m) cc_final: 0.8134 (m)
  outliers start: 13
  outliers final: 10
  residues processed: 190
  average time/residue: 0.1787
  time to fit residues: 45.2780
Evaluate side-chains
  185 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 174
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  149 ASP
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  422 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0980
   chunk 48 optimal weight:    0.4980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
A 601 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.116130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.103896 restraints weight = 9667.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.16
r_work: 0.3192 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   6638  Z= 0.276
  Angle     :  0.633  10.150   9018  Z= 0.319
  Chirality :  0.045   0.255    943
  Planarity :  0.006   0.117   1169
  Dihedral  :  5.760  57.902    929
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  6.10 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 18.05 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.30), residues: 787
  helix:  1.09 (0.27), residues: 391
  sheet:  0.06 (0.65), residues: 53
  loop : -1.42 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 477 
 HIS   0.006   0.001   HIS A 378 
 PHE   0.013   0.001   PHE A 308 
 TYR   0.019   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 219 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 186
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8454 (tp30) cc_final: 0.8161 (tp30)
REVERT: A  114 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7757 (mmtt)
REVERT: A  402 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7191 (mm-30)
REVERT: A  455 MET cc_start: 0.8430 (tmm) cc_final: 0.8067 (tmm)
REVERT: A  470 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8473 (tttp)
REVERT: A  479 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7801 (tm-30)
REVERT: A  508 ASN cc_start: 0.7950 (m-40) cc_final: 0.7717 (t0)
REVERT: A  556 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8283 (mtpp)
REVERT: B  438 SER cc_start: 0.8124 (t) cc_final: 0.7832 (t)
REVERT: B  443 SER cc_start: 0.8488 (m) cc_final: 0.8239 (m)
  outliers start: 12
  outliers final: 8
  residues processed: 193
  average time/residue: 0.1868
  time to fit residues: 48.0294
Evaluate side-chains
  192 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 183
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  362 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 35 optimal weight:    0.4980
   chunk 64 optimal weight:    0.6980
   chunk 20 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
A 345 HIS
A 601 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.115463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.103366 restraints weight = 9871.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.19
r_work: 0.3178 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   6638  Z= 0.289
  Angle     :  0.642  10.133   9018  Z= 0.321
  Chirality :  0.045   0.257    943
  Planarity :  0.006   0.118   1169
  Dihedral  :  5.815  58.133    929
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  5.59 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 18.63 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.30), residues: 787
  helix:  1.02 (0.27), residues: 392
  sheet:  0.10 (0.65), residues: 53
  loop : -1.44 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 378 
 PHE   0.013   0.001   PHE A 308 
 TYR   0.019   0.001   TYR A 385 
 ARG   0.008   0.000   ARG A 577 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 178
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8452 (tp30) cc_final: 0.8154 (tp30)
REVERT: A   78 LYS cc_start: 0.8630 (tptm) cc_final: 0.8262 (tptm)
REVERT: A  402 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7397 (mm-30)
REVERT: A  455 MET cc_start: 0.8479 (tmm) cc_final: 0.8133 (tmm)
REVERT: A  470 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8471 (tttp)
REVERT: A  479 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7875 (tm-30)
REVERT: A  508 ASN cc_start: 0.7976 (m-40) cc_final: 0.7731 (t0)
REVERT: A  556 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8286 (mtpp)
REVERT: B  347 PHE cc_start: 0.8453 (m-10) cc_final: 0.8097 (m-80)
REVERT: B  438 SER cc_start: 0.8134 (t) cc_final: 0.7897 (t)
REVERT: B  443 SER cc_start: 0.8495 (m) cc_final: 0.8252 (m)
  outliers start: 11
  outliers final: 8
  residues processed: 184
  average time/residue: 0.2071
  time to fit residues: 51.4086
Evaluate side-chains
  188 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 179
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0870
   chunk 39 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0970
   chunk 69 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
A 601 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.116624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.104433 restraints weight = 9967.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 2.22
r_work: 0.3193 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   6638  Z= 0.238
  Angle     :  0.626  10.093   9018  Z= 0.313
  Chirality :  0.045   0.257    943
  Planarity :  0.006   0.118   1169
  Dihedral  :  5.777  58.201    929
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  5.72 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.92 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.30), residues: 787
  helix:  1.05 (0.27), residues: 392
  sheet:  0.15 (0.66), residues: 53
  loop : -1.40 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 378 
 PHE   0.012   0.001   PHE A 308 
 TYR   0.018   0.001   TYR A 385 
 ARG   0.007   0.000   ARG A 577 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 176
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8457 (tp30) cc_final: 0.8161 (tp30)
REVERT: A   78 LYS cc_start: 0.8620 (tptm) cc_final: 0.8247 (tptm)
REVERT: A  287 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7935 (mm-40)
REVERT: A  402 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7380 (mm-30)
REVERT: A  455 MET cc_start: 0.8474 (tmm) cc_final: 0.8135 (tmm)
REVERT: A  470 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8456 (tttp)
REVERT: A  479 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7827 (tm-30)
REVERT: A  508 ASN cc_start: 0.7967 (m-40) cc_final: 0.7753 (t0)
REVERT: A  556 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8267 (mtpp)
REVERT: B  443 SER cc_start: 0.8475 (m) cc_final: 0.8234 (m)
  outliers start: 13
  outliers final: 11
  residues processed: 181
  average time/residue: 0.1769
  time to fit residues: 42.9367
Evaluate side-chains
  190 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0060
   chunk 45 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0000
   chunk 46 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.4000

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.117011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.104797 restraints weight = 9876.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.21
r_work: 0.3202 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   6638  Z= 0.231
  Angle     :  0.660  14.738   9018  Z= 0.327
  Chirality :  0.046   0.368    943
  Planarity :  0.006   0.118   1169
  Dihedral  :  5.797  57.970    929
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  4.96 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.92 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.30), residues: 787
  helix:  1.17 (0.27), residues: 385
  sheet:  0.22 (0.65), residues: 53
  loop : -1.44 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A 378 
 PHE   0.012   0.001   PHE B 486 
 TYR   0.018   0.001   TYR A 385 
 ARG   0.007   0.000   ARG A 577 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 173
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8453 (tp30) cc_final: 0.8158 (tp30)
REVERT: A   78 LYS cc_start: 0.8617 (tptm) cc_final: 0.8246 (tptm)
REVERT: A  287 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7893 (mm-40)
REVERT: A  455 MET cc_start: 0.8461 (tmm) cc_final: 0.8118 (tmm)
REVERT: A  470 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8471 (tttp)
REVERT: A  479 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7828 (tm-30)
REVERT: A  508 ASN cc_start: 0.7975 (m-40) cc_final: 0.7760 (t0)
REVERT: A  556 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8256 (mtpp)
REVERT: B  443 SER cc_start: 0.8474 (m) cc_final: 0.8234 (m)
  outliers start: 13
  outliers final: 10
  residues processed: 178
  average time/residue: 0.1751
  time to fit residues: 41.8449
Evaluate side-chains
  184 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 173
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLU
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0770
   chunk 43 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0770
   chunk 42 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.4896

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.116088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.103750 restraints weight = 10030.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.23
r_work: 0.3189 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   6638  Z= 0.256
  Angle     :  0.674  14.844   9018  Z= 0.336
  Chirality :  0.046   0.353    943
  Planarity :  0.006   0.119   1169
  Dihedral  :  5.825  57.742    929
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  5.84 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.21 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.30), residues: 787
  helix:  1.06 (0.27), residues: 392
  sheet:  0.36 (0.65), residues: 53
  loop : -1.39 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A 378 
 PHE   0.013   0.001   PHE A 308 
 TYR   0.018   0.001   TYR A 385 
 ARG   0.007   0.000   ARG A 577 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4649.70 seconds
wall clock time: 83 minutes 2.31 seconds (4982.31 seconds total)