Starting phenix.real_space_refine
on Tue Mar  3 14:23:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bw8_30230/03_2026/7bw8_30230.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bw8_30230/03_2026/7bw8_30230.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bw8_30230/03_2026/7bw8_30230.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bw8_30230/03_2026/7bw8_30230.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bw8_30230/03_2026/7bw8_30230.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bw8_30230/03_2026/7bw8_30230.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      46      5.16       5
     C    3847      2.51       5
     N    1026      2.21       5
     O    1102      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 79 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6021
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4469
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4469
          Classifications: {'peptide': 551}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 525}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 1176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1176
          Classifications: {'peptide': 138}
          Link IDs: {'PTRANS': 10, 'TRANS': 127}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 376
          Classifications: {'peptide': 48}
          Link IDs: {'PTRANS': 1, 'TRANS': 46}
          Chain breaks: 1
  Time building chain proxies: 1.28, per 1000 atoms: 0.21
  Number of scatterers: 6021
  At special positions: 0
  Unit cell: (83.57, 94.53, 108.23, 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      46     16.00
     O    1102      8.00
     N    1026      7.00
     C    3847      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   8 " - pdb=" SG  CYS A  26 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 192 " - pdb=" SG  CYS A 201 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 196 " - pdb=" SG  CYS A 207 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 208 " - pdb=" SG  CYS A 216 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 225 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS A 237 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 253 " distance=1.71
    Simple disulfide: pdb=" SG  CYS A 259 " - pdb=" SG  CYS A 284 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 266 " - pdb=" SG  CYS A 274 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 301 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 312 " - pdb=" SG  CYS A 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 435 " - pdb=" SG  CYS A 468 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   7 " - pdb=" SG  CYS D  62 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  19 " - pdb=" SG  CYS D  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  61 " - pdb=" SG  CYS D  66 " 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
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 301.4 milliseconds
  

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1398

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 11 sheets defined
      15.2% alpha, 13.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 20
      removed outlier: 3.854A  pdb=" N   LEU A  20 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 49
    Processing helix  chain 'A' and resid 139 through 143
      removed outlier: 3.625A  pdb=" N   ASP A 142 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 267
      removed outlier: 3.861A  pdb=" N   CYS A 259 " --> pdb=" O   ASN A 255 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   CYS A 266 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 318
      removed outlier: 3.656A  pdb=" N   GLY A 317 " --> pdb=" O   LEU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 328
    Processing helix  chain 'A' and resid 350 through 358
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 4.108A  pdb=" N   GLY A 447 " --> pdb=" O   GLU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 500
      removed outlier: 3.553A  pdb=" N   LEU A 500 " --> pdb=" O   PHE A 497 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 692 through 697
    Processing helix  chain 'C' and resid 697 through 713
      removed outlier: 4.209A  pdb=" N   LYS C 703 " --> pdb=" O   SER C 699 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 19
      removed outlier: 3.874A  pdb=" N   CYS D  19 " --> pdb=" O   LEU D  15 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 62
    Processing helix  chain 'D' and resid 69 through 74
      removed outlier: 3.944A  pdb=" N   ASN D  73 " --> pdb=" O   TYR D  69 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14
      removed outlier: 6.128A  pdb=" N   ILE A  13 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   MET A  38 " --> pdb=" O   ILE A  13 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   VAL A  66 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LEU A  63 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   MET A  98 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   TYR A  67 " --> pdb=" O   MET A  98 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   LEU A  93 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   GLU A 120 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   ILE A  95 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57
      removed outlier: 3.625A  pdb=" N   ILE A  57 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ILE A  82 " --> pdb=" O   ASN A 111 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 248
    Processing sheet with id=AA4, first strand: chain 'A' and resid 278 through 279
    Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 294
    Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 336
      removed outlier: 3.575A  pdb=" N   ILE A 336 " --> pdb=" O   GLU A 363 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 387 through 388
    Processing sheet with id=AA8, first strand: chain 'A' and resid 474 through 479
      removed outlier: 6.233A  pdb=" N   PHE A 475 " --> pdb=" O   GLU A 490 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   GLU A 490 " --> pdb=" O   PHE A 475 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 530 through 534
      removed outlier: 3.750A  pdb=" N   THR A 530 " --> pdb=" O   TYR A 507 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   TYR A 507 " --> pdb=" O   THR A 530 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   TYR A 562 " --> pdb=" O   VAL A 588 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL A 588 " --> pdb=" O   TYR A 562 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   VAL A 566 " --> pdb=" O   ASP A 584 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   ASP A 584 " --> pdb=" O   VAL A 566 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   THR A 568 " --> pdb=" O   LYS A 582 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   LYS A 582 " --> pdb=" O   THR A 568 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 485 through 486
      removed outlier: 3.622A  pdb=" N   ILE C 485 " --> pdb=" O   MET C 553 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 531 through 534
      removed outlier: 3.574A  pdb=" N   VAL C 532 " --> pdb=" O   LEU C 505 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   THR C 560 " --> pdb=" O   THR C 590 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   VAL C 566 " --> pdb=" O   ASP C 584 " (cutoff:3.500A)
      removed outlier: 5.604A  pdb=" N   ASP C 584 " --> pdb=" O   VAL C 566 " (cutoff:3.500A)

    101 hydrogen bonds defined for protein.
    258 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.91

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1478
        1.33 -     1.46: 1574
        1.46 -     1.58: 3063
        1.58 -     1.71: 0
        1.71 -     1.83: 57
  Bond restraints: 6172
  Sorted by residual:
  bond pdb=" N   GLN A 589 "
       pdb=" CA  GLN A 589 "
    ideal  model  delta    sigma   weight residual
    1.456  1.498 -0.042 1.27e-02 6.20e+03 1.08e+01
  bond pdb=" C   PRO C 536 "
       pdb=" N   PRO C 537 "
    ideal  model  delta    sigma   weight residual
    1.335  1.307  0.028 8.70e-03 1.32e+04 1.04e+01
  bond pdb=" N   TYR A 477 "
       pdb=" CA  TYR A 477 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.25e-02 6.40e+03 7.83e+00
  bond pdb=" N   VAL D  12 "
       pdb=" CA  VAL D  12 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.033 1.21e-02 6.83e+03 7.33e+00
  bond pdb=" N   ARG A 252 "
       pdb=" CA  ARG A 252 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.27e-02 6.20e+03 7.20e+00
  ... (remaining 6167 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 7700
        2.46 -     4.92: 584
        4.92 -     7.38: 69
        7.38 -     9.84: 7
        9.84 -    12.29: 3
  Bond angle restraints: 8363
  Sorted by residual:
  angle pdb=" N   VAL A 445 "
        pdb=" CA  VAL A 445 "
        pdb=" C   VAL A 445 "
      ideal   model   delta    sigma   weight residual
     112.29  108.64    3.65 9.40e-01 1.13e+00 1.51e+01
  angle pdb=" N   GLY C 555 "
        pdb=" CA  GLY C 555 "
        pdb=" C   GLY C 555 "
      ideal   model   delta    sigma   weight residual
     113.18  122.28   -9.10 2.37e+00 1.78e-01 1.47e+01
  angle pdb=" CA  TYR D  16 "
        pdb=" CB  TYR D  16 "
        pdb=" CG  TYR D  16 "
      ideal   model   delta    sigma   weight residual
     113.90  107.05    6.85 1.80e+00 3.09e-01 1.45e+01
  angle pdb=" CA  TRP C 559 "
        pdb=" C   TRP C 559 "
        pdb=" O   TRP C 559 "
      ideal   model   delta    sigma   weight residual
     122.27  117.87    4.40 1.16e+00 7.43e-01 1.44e+01
  angle pdb=" C   THR C 560 "
        pdb=" N   GLN C 561 "
        pdb=" CA  GLN C 561 "
      ideal   model   delta    sigma   weight residual
     120.87  126.15   -5.28 1.42e+00 4.96e-01 1.38e+01
  ... (remaining 8358 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3109
       17.96 -    35.92: 482
       35.92 -    53.88: 106
       53.88 -    71.84: 13
       71.84 -    89.80: 8
  Dihedral angle restraints: 3718
    sinusoidal: 1557
      harmonic: 2161
  Sorted by residual:
  dihedral pdb=" CB  CYS A 228 "
           pdb=" SG  CYS A 228 "
           pdb=" SG  CYS A 237 "
           pdb=" CB  CYS A 237 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.14  -88.86     1      1.00e+01 1.00e-02 9.41e+01
  dihedral pdb=" CB  CYS D  61 "
           pdb=" SG  CYS D  61 "
           pdb=" SG  CYS D  66 "
           pdb=" CB  CYS D  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    6.87   86.13     1      1.00e+01 1.00e-02 8.95e+01
  dihedral pdb=" CB  CYS D  19 "
           pdb=" SG  CYS D  19 "
           pdb=" SG  CYS D  75 "
           pdb=" CB  CYS D  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.84  -67.84     1      1.00e+01 1.00e-02 5.98e+01
  ... (remaining 3715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 574
       0.059 -    0.118: 240
       0.118 -    0.176: 74
       0.176 -    0.235: 14
       0.235 -    0.294: 3
  Chirality restraints: 905
  Sorted by residual:
  chirality pdb=" CB  VAL A 515 "
            pdb=" CA  VAL A 515 "
            pdb=" CG1 VAL A 515 "
            pdb=" CG2 VAL A 515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CA  TYR D  16 "
            pdb=" N   TYR D  16 "
            pdb=" C   TYR D  16 "
            pdb=" CB  TYR D  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  ASN A 541 "
            pdb=" N   ASN A 541 "
            pdb=" C   ASN A 541 "
            pdb=" CB  ASN A 541 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  ... (remaining 902 not shown)

  Planarity restraints: 1070
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  16 "   -0.036 2.00e-02 2.50e+03   3.14e-02 1.98e+01
        pdb=" CG  TYR D  16 "    0.077 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  16 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  16 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  16 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  16 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  16 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D  16 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 579 "    0.023 2.00e-02 2.50e+03   2.46e-02 1.21e+01
        pdb=" CG  TYR A 579 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 579 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 579 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 579 "    0.025 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 579 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 579 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 579 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 337 "   -0.017 2.00e-02 2.50e+03   3.37e-02 1.13e+01
        pdb=" CG  ASN A 337 "    0.058 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 337 "   -0.022 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 337 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1067 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.56: 164
        2.56 -     3.14: 5673
        3.14 -     3.73: 9188
        3.73 -     4.31: 12124
        4.31 -     4.90: 18616
  Nonbonded interactions: 45765
  Sorted by model distance:
  nonbonded pdb=" O   SER A 540 "
            pdb=" OD1 ASN A 541 "
     model   vdw
     1.974 3.040
  nonbonded pdb=" OD1 ASN A 541 "
            pdb=" OD1 ASP A 542 "
     model   vdw
     2.004 3.040
  nonbonded pdb=" NZ  LYS C 557 "
            pdb=" OG1 THR C 560 "
     model   vdw
     2.051 3.120
  nonbonded pdb=" O   GLU A 443 "
            pdb=" OG  SER A 446 "
     model   vdw
     2.104 3.040
  nonbonded pdb=" O   THR A 571 "
            pdb=" OG1 THR A 578 "
     model   vdw
     2.109 3.040
  ... (remaining 45760 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.990
  Find NCS groups from input model:        0.020
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6591
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      :  0.010   0.322   6187  Z= 0.511
  Angle     :  1.402  15.154   8393  Z= 0.798
  Chirality :  0.071   0.294    905
  Planarity :  0.008   0.061   1070
  Dihedral  : 17.387  89.796   2275
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 49.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.25 %
    Favored  : 77.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.01 (0.26), residues: 719
  helix: -2.92 (0.42), residues: 92
  sheet: -2.21 (0.53), residues: 80
  loop : -3.94 (0.23), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG A 118 
 TYR   0.077   0.005   TYR D  16 
 PHE   0.038   0.005   PHE A 231 
 TRP   0.046   0.004   TRP A 183 
 HIS   0.022   0.004   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00943 ( 6172)
  covalent geometry    : angle       1.37647 ( 8363)
  SS BOND              : bond        0.08392 (   15)
  SS BOND              : angle       4.62743 (   30)
  hydrogen bonds       : bond        0.23539 (  101)
  hydrogen bonds       : angle      10.90443 (  258)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.8079 (mmt180) cc_final: 0.7387 (mmt90)
REVERT: A  221 ASP cc_start: 0.7618 (m-30) cc_final: 0.7305 (p0)
REVERT: A  310 LYS cc_start: 0.7883 (ttpp) cc_final: 0.7662 (pttp)
REVERT: A  454 ARG cc_start: 0.7256 (mtt-85) cc_final: 0.6859 (mtt-85)
REVERT: A  504 MET cc_start: 0.3325 (mmm) cc_final: 0.2903 (mmm)
REVERT: A  553 MET cc_start: 0.8012 (mmm) cc_final: 0.7723 (mmm)
REVERT: C  567 LYS cc_start: 0.3880 (mttm) cc_final: 0.2171 (ptmt)
REVERT: C  695 GLU cc_start: 0.8748 (pm20) cc_final: 0.8295 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.0874
  time to fit residues: 17.2923
Evaluate side-chains
  137 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0040
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 GLN
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 GLN
D   4 GLN
D  76 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.166322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.146674 restraints weight = 16162.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.150347 restraints weight = 9654.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.152854 restraints weight = 6582.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.154580 restraints weight = 4884.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.155829 restraints weight = 3872.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6346
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6187  Z= 0.180
  Angle     :  0.938  10.036   8393  Z= 0.474
  Chirality :  0.054   0.216    905
  Planarity :  0.006   0.072   1070
  Dihedral  :  7.628  26.136    805
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 21.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.60 %
    Favored  : 85.40 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.22 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.56 (0.27), residues: 719
  helix: -2.59 (0.45), residues: 96
  sheet: -2.51 (0.45), residues: 102
  loop : -3.51 (0.24), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 252 
 TYR   0.042   0.002   TYR D  16 
 PHE   0.018   0.002   PHE A 506 
 TRP   0.020   0.002   TRP A 551 
 HIS   0.012   0.002   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6172)
  covalent geometry    : angle       0.93257 ( 8363)
  SS BOND              : bond        0.00818 (   15)
  SS BOND              : angle       1.95692 (   30)
  hydrogen bonds       : bond        0.05633 (  101)
  hydrogen bonds       : angle       8.47818 (  258)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 168
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.6256 (pmm) cc_final: 0.5769 (pmm)
REVERT: A  102 LYS cc_start: 0.8683 (pttm) cc_final: 0.8430 (mmtp)
REVERT: A  379 LEU cc_start: 0.9560 (tp) cc_final: 0.9271 (tp)
REVERT: A  383 ARG cc_start: 0.8428 (mtt180) cc_final: 0.7930 (mtm110)
REVERT: A  412 TRP cc_start: 0.8095 (m-90) cc_final: 0.7851 (m-90)
REVERT: A  465 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7274 (mp10)
REVERT: A  553 MET cc_start: 0.7814 (mmm) cc_final: 0.7511 (mmm)
REVERT: C  533 ASP cc_start: 0.7457 (p0) cc_final: 0.6832 (p0)
REVERT: C  551 TRP cc_start: 0.7840 (t-100) cc_final: 0.7409 (t-100)
REVERT: C  591 ASP cc_start: 0.5328 (t0) cc_final: 0.4842 (t0)
REVERT: D   13 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8316 (mt-10)
REVERT: D   76 ASN cc_start: 0.7889 (m-40) cc_final: 0.6972 (m-40)
  outliers start: 20
  outliers final: 14
  residues processed: 176
  average time/residue: 0.0814
  time to fit residues: 18.2581
Evaluate side-chains
  170 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  416 LYS
Chi-restraints excluded: chain A residue  437 SER
Chi-restraints excluded: chain A residue  465 GLN
Chi-restraints excluded: chain A residue  507 TYR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  590 THR
Chi-restraints excluded: chain C residue  692 ILE
Chi-restraints excluded: chain D residue   27 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0040
   chunk 52 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    1.9398

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 711 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.162900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.144248 restraints weight = 16468.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.148371 restraints weight = 10407.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.150829 restraints weight = 6398.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.152578 restraints weight = 4510.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.152772 restraints weight = 3756.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.4226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6484
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6187  Z= 0.193
  Angle     :  0.861   9.753   8393  Z= 0.440
  Chirality :  0.052   0.217    905
  Planarity :  0.006   0.055   1070
  Dihedral  :  7.322  35.174    805
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 24.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.44 %
    Favored  : 84.56 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 21.39 %
    Favored  : 73.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.45 (0.27), residues: 719
  helix: -2.44 (0.46), residues: 97
  sheet: -2.52 (0.47), residues: 98
  loop : -3.42 (0.24), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 409 
 TYR   0.034   0.002   TYR D  16 
 PHE   0.016   0.002   PHE A 428 
 TRP   0.013   0.002   TRP A 133 
 HIS   0.009   0.002   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 6172)
  covalent geometry    : angle       0.85494 ( 8363)
  SS BOND              : bond        0.00556 (   15)
  SS BOND              : angle       1.96922 (   30)
  hydrogen bonds       : bond        0.04928 (  101)
  hydrogen bonds       : angle       8.19068 (  258)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7917 (mm-30)
REVERT: A  102 LYS cc_start: 0.8605 (pttm) cc_final: 0.8404 (mmtp)
REVERT: A  383 ARG cc_start: 0.8269 (mtt180) cc_final: 0.7859 (mtm110)
REVERT: A  465 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7635 (mp10)
REVERT: A  553 MET cc_start: 0.7803 (mmm) cc_final: 0.7413 (mmm)
REVERT: C  486 LEU cc_start: 0.8665 (tp) cc_final: 0.8457 (mp)
REVERT: C  533 ASP cc_start: 0.7596 (p0) cc_final: 0.7184 (p0)
REVERT: C  551 TRP cc_start: 0.7893 (t-100) cc_final: 0.7476 (t-100)
REVERT: C  591 ASP cc_start: 0.4918 (t0) cc_final: 0.4418 (t0)
REVERT: D   13 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8332 (mt-10)
REVERT: D   74 TYR cc_start: 0.7059 (t80) cc_final: 0.6744 (t80)
REVERT: D   76 ASN cc_start: 0.8480 (m-40) cc_final: 0.7573 (m-40)
  outliers start: 33
  outliers final: 24
  residues processed: 170
  average time/residue: 0.0761
  time to fit residues: 16.7005
Evaluate side-chains
  172 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ASP
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  437 SER
Chi-restraints excluded: chain A residue  465 GLN
Chi-restraints excluded: chain A residue  482 PHE
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  507 TYR
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain C residue  572 PHE
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  590 THR
Chi-restraints excluded: chain C residue  704 THR
Chi-restraints excluded: chain D residue   10 HIS
Chi-restraints excluded: chain D residue   27 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 43 optimal weight:    0.1980
   chunk 34 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 13 optimal weight:    0.3980
   chunk 0 optimal weight:    9.9990
   chunk 3 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 462 ASN ** 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 = 0.4375 r_free = 0.4375 target = 0.165596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.146970 restraints weight = 16470.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.151366 restraints weight = 10428.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.154465 restraints weight = 6249.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.155034 restraints weight = 4246.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.156219 restraints weight = 3677.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6398
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6187  Z= 0.149
  Angle     :  0.808   8.839   8393  Z= 0.404
  Chirality :  0.050   0.224    905
  Planarity :  0.006   0.078   1070
  Dihedral  :  6.816  30.660    805
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.35 %
    Favored  : 86.65 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 24.93 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.00 (0.28), residues: 719
  helix: -2.12 (0.49), residues: 94
  sheet: -2.01 (0.53), residues: 86
  loop : -3.14 (0.25), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  86 
 TYR   0.026   0.002   TYR D  16 
 PHE   0.017   0.002   PHE A 428 
 TRP   0.013   0.002   TRP A 551 
 HIS   0.008   0.001   HIS D  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6172)
  covalent geometry    : angle       0.80163 ( 8363)
  SS BOND              : bond        0.00584 (   15)
  SS BOND              : angle       1.82724 (   30)
  hydrogen bonds       : bond        0.04283 (  101)
  hydrogen bonds       : angle       7.60160 (  258)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 151
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.6779 (pmm) cc_final: 0.6455 (pmm)
REVERT: A   83 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7163 (mtp180)
REVERT: A  313 HIS cc_start: 0.3063 (OUTLIER) cc_final: 0.1663 (m-70)
REVERT: A  383 ARG cc_start: 0.8379 (mtt180) cc_final: 0.7943 (mtm110)
REVERT: A  465 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7312 (mp10)
REVERT: A  482 PHE cc_start: 0.1171 (OUTLIER) cc_final: 0.0286 (t80)
REVERT: A  500 LEU cc_start: 0.8149 (pp) cc_final: 0.7777 (tt)
REVERT: A  553 MET cc_start: 0.7894 (mmm) cc_final: 0.7426 (mmm)
REVERT: C  533 ASP cc_start: 0.7624 (p0) cc_final: 0.7399 (p0)
REVERT: C  551 TRP cc_start: 0.7763 (t-100) cc_final: 0.7351 (t-100)
REVERT: C  559 TRP cc_start: 0.0273 (OUTLIER) cc_final: -0.2928 (m-10)
REVERT: C  587 TYR cc_start: 0.6566 (OUTLIER) cc_final: 0.5907 (m-80)
REVERT: C  591 ASP cc_start: 0.5264 (t0) cc_final: 0.4730 (t0)
REVERT: D   13 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8263 (mt-10)
  outliers start: 34
  outliers final: 21
  residues processed: 169
  average time/residue: 0.0825
  time to fit residues: 17.8784
Evaluate side-chains
  171 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  133 TRP
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  246 TYR
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  437 SER
Chi-restraints excluded: chain A residue  465 GLN
Chi-restraints excluded: chain A residue  482 PHE
Chi-restraints excluded: chain A residue  507 TYR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain C residue  559 TRP
Chi-restraints excluded: chain C residue  572 PHE
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  579 TYR
Chi-restraints excluded: chain C residue  587 TYR
Chi-restraints excluded: chain C residue  692 ILE
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   27 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0270
   chunk 15 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 546 GLN
** D  70 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 = 0.4400 r_free = 0.4400 target = 0.167862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.148688 restraints weight = 16195.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.153201 restraints weight = 9969.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.156255 restraints weight = 5947.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.157022 restraints weight = 4101.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.158040 restraints weight = 3456.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.4274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6345
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6187  Z= 0.133
  Angle     :  0.789   9.583   8393  Z= 0.392
  Chirality :  0.049   0.201    905
  Planarity :  0.005   0.054   1070
  Dihedral  :  6.397  26.295    805
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 16.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.38 %
    Favored  : 87.62 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 27.88 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.63 (0.30), residues: 719
  helix: -1.92 (0.51), residues: 93
  sheet: -1.72 (0.55), residues: 91
  loop : -2.87 (0.26), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  86 
 TYR   0.021   0.002   TYR D  16 
 PHE   0.015   0.002   PHE C 714 
 TRP   0.010   0.001   TRP A 251 
 HIS   0.007   0.001   HIS D  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6172)
  covalent geometry    : angle       0.78386 ( 8363)
  SS BOND              : bond        0.00493 (   15)
  SS BOND              : angle       1.65091 (   30)
  hydrogen bonds       : bond        0.03838 (  101)
  hydrogen bonds       : angle       7.37184 (  258)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 151
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ARG cc_start: 0.6733 (ttm-80) cc_final: 0.6189 (tpp-160)
REVERT: A   83 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7196 (mtp180)
REVERT: A  102 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7886 (mmtt)
REVERT: A  125 LEU cc_start: 0.8628 (mt) cc_final: 0.8394 (mt)
REVERT: A  265 LYS cc_start: 0.7135 (tmtt) cc_final: 0.6861 (tppt)
REVERT: A  313 HIS cc_start: 0.3177 (OUTLIER) cc_final: 0.1846 (m-70)
REVERT: A  383 ARG cc_start: 0.8384 (mtt180) cc_final: 0.7915 (mtm110)
REVERT: A  465 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7180 (mp10)
REVERT: A  482 PHE cc_start: 0.0667 (OUTLIER) cc_final: 0.0190 (t80)
REVERT: A  500 LEU cc_start: 0.8126 (pp) cc_final: 0.7848 (tt)
REVERT: A  553 MET cc_start: 0.7816 (mmm) cc_final: 0.7375 (mmm)
REVERT: C  551 TRP cc_start: 0.7619 (t-100) cc_final: 0.7237 (t-100)
REVERT: C  567 LYS cc_start: 0.3173 (ttmt) cc_final: 0.2884 (ttmt)
REVERT: C  569 LEU cc_start: 0.8916 (mt) cc_final: 0.8678 (mp)
REVERT: C  587 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.5668 (m-80)
REVERT: C  591 ASP cc_start: 0.4895 (t0) cc_final: 0.4527 (t0)
REVERT: D   76 ASN cc_start: 0.8567 (m-40) cc_final: 0.8227 (m110)
  outliers start: 33
  outliers final: 22
  residues processed: 172
  average time/residue: 0.0834
  time to fit residues: 18.3590
Evaluate side-chains
  166 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 139
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  133 TRP
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  251 TRP
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  328 GLN
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  465 GLN
Chi-restraints excluded: chain A residue  482 PHE
Chi-restraints excluded: chain A residue  507 TYR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain C residue  572 PHE
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  587 TYR
Chi-restraints excluded: chain C residue  590 THR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   27 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 56 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0030
   chunk 15 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0870
   chunk 66 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 17 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.4168

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 462 ASN
D  70 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.168784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.149717 restraints weight = 15903.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.154260 restraints weight = 10028.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.157278 restraints weight = 5993.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.158272 restraints weight = 4144.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.159785 restraints weight = 3394.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6305
moved from start:          0.4367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6187  Z= 0.130
  Angle     :  0.785  11.020   8393  Z= 0.387
  Chirality :  0.048   0.188    905
  Planarity :  0.005   0.078   1070
  Dihedral  :  6.176  22.908    805
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.54 %
    Favored  : 88.46 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 28.32 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.42 (0.30), residues: 719
  helix: -1.92 (0.50), residues: 93
  sheet: -1.51 (0.56), residues: 93
  loop : -2.70 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 135 
 TYR   0.020   0.002   TYR D  16 
 PHE   0.015   0.001   PHE C 714 
 TRP   0.011   0.001   TRP A 251 
 HIS   0.007   0.001   HIS D  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6172)
  covalent geometry    : angle       0.78053 ( 8363)
  SS BOND              : bond        0.00394 (   15)
  SS BOND              : angle       1.55595 (   30)
  hydrogen bonds       : bond        0.03726 (  101)
  hydrogen bonds       : angle       7.14698 (  258)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 144
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7949 (mm-30)
REVERT: A   83 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7046 (mtp180)
REVERT: A  125 LEU cc_start: 0.8510 (mt) cc_final: 0.8276 (mt)
REVERT: A  313 HIS cc_start: 0.3026 (OUTLIER) cc_final: 0.1186 (m-70)
REVERT: A  383 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7936 (mtm110)
REVERT: A  465 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7341 (mp10)
REVERT: A  482 PHE cc_start: 0.0440 (OUTLIER) cc_final: 0.0072 (t80)
REVERT: A  553 MET cc_start: 0.7725 (mmm) cc_final: 0.7226 (mmm)
REVERT: C  551 TRP cc_start: 0.7409 (t-100) cc_final: 0.7079 (t-100)
REVERT: C  559 TRP cc_start: 0.0680 (OUTLIER) cc_final: -0.3107 (m-10)
REVERT: C  587 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.5547 (m-80)
REVERT: C  591 ASP cc_start: 0.4952 (t0) cc_final: 0.4656 (t0)
REVERT: D   13 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8108 (mt-10)
  outliers start: 34
  outliers final: 20
  residues processed: 167
  average time/residue: 0.0807
  time to fit residues: 17.3385
Evaluate side-chains
  163 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  251 TRP
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  405 ASN
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  437 SER
Chi-restraints excluded: chain A residue  465 GLN
Chi-restraints excluded: chain A residue  474 LYS
Chi-restraints excluded: chain A residue  482 PHE
Chi-restraints excluded: chain A residue  507 TYR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  566 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain C residue  559 TRP
Chi-restraints excluded: chain C residue  572 PHE
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  587 TYR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   27 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0270
   chunk 35 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 62 optimal weight:    0.3980
   chunk 1 optimal weight:    0.0000
   chunk 36 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0470
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.2740

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  76 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.171406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.152279 restraints weight = 15904.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.156797 restraints weight = 9734.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.159652 restraints weight = 5784.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.160979 restraints weight = 4090.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.162416 restraints weight = 3172.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6208
moved from start:          0.4839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6187  Z= 0.130
  Angle     :  0.777   9.068   8393  Z= 0.382
  Chirality :  0.047   0.222    905
  Planarity :  0.005   0.046   1070
  Dihedral  :  5.860  23.180    805
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.71 %
    Favored  : 89.29 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 29.79 %
    Favored  : 64.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.16 (0.30), residues: 719
  helix: -1.71 (0.53), residues: 90
  sheet: -1.33 (0.59), residues: 87
  loop : -2.51 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 135 
 TYR   0.019   0.001   TYR D  16 
 PHE   0.016   0.001   PHE A  39 
 TRP   0.016   0.001   TRP A 551 
 HIS   0.007   0.001   HIS D  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6172)
  covalent geometry    : angle       0.77315 ( 8363)
  SS BOND              : bond        0.00356 (   15)
  SS BOND              : angle       1.52714 (   30)
  hydrogen bonds       : bond        0.03362 (  101)
  hydrogen bonds       : angle       6.84128 (  258)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 150
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8129 (mm-30)
REVERT: A   83 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7119 (mtp180)
REVERT: A  125 LEU cc_start: 0.8376 (mt) cc_final: 0.8144 (mt)
REVERT: A  239 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8212 (mm-30)
REVERT: A  313 HIS cc_start: 0.2682 (OUTLIER) cc_final: 0.2221 (t-90)
REVERT: A  357 ASN cc_start: 0.7675 (t0) cc_final: 0.7390 (t0)
REVERT: A  383 ARG cc_start: 0.8313 (mtt180) cc_final: 0.7902 (mtm110)
REVERT: A  465 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7157 (mp10)
REVERT: A  500 LEU cc_start: 0.7817 (pp) cc_final: 0.7600 (tt)
REVERT: A  551 TRP cc_start: 0.6121 (t-100) cc_final: 0.5422 (t-100)
REVERT: A  560 THR cc_start: 0.3412 (OUTLIER) cc_final: 0.3058 (p)
REVERT: C  484 LYS cc_start: 0.8152 (mptt) cc_final: 0.7922 (mmtt)
REVERT: C  551 TRP cc_start: 0.7369 (t-100) cc_final: 0.7069 (t-100)
REVERT: C  559 TRP cc_start: 0.0596 (OUTLIER) cc_final: -0.3174 (m-10)
REVERT: C  587 TYR cc_start: 0.6516 (OUTLIER) cc_final: 0.5582 (m-80)
REVERT: C  591 ASP cc_start: 0.5306 (t0) cc_final: 0.5054 (t0)
REVERT: C  695 GLU cc_start: 0.8380 (pm20) cc_final: 0.8100 (pm20)
  outliers start: 36
  outliers final: 21
  residues processed: 175
  average time/residue: 0.0750
  time to fit residues: 17.1074
Evaluate side-chains
  162 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  251 TRP
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  465 GLN
Chi-restraints excluded: chain A residue  474 LYS
Chi-restraints excluded: chain A residue  507 TYR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  591 ASP
Chi-restraints excluded: chain C residue  559 TRP
Chi-restraints excluded: chain C residue  570 VAL
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  587 TYR
Chi-restraints excluded: chain D residue   27 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 54 optimal weight:    0.3980
   chunk 71 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0770
   chunk 49 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0070
   chunk 65 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** 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 = 0.4425 r_free = 0.4425 target = 0.170171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.150895 restraints weight = 16074.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.155576 restraints weight = 9898.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.158498 restraints weight = 5872.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.159616 restraints weight = 4082.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.161254 restraints weight = 3260.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6242
moved from start:          0.5145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6187  Z= 0.129
  Angle     :  0.814  12.675   8393  Z= 0.392
  Chirality :  0.048   0.215    905
  Planarity :  0.005   0.074   1070
  Dihedral  :  5.834  22.392    805
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.71 %
    Favored  : 89.29 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 30.53 %
    Favored  : 64.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.18 (0.30), residues: 719
  helix: -1.89 (0.51), residues: 94
  sheet: -1.04 (0.60), residues: 79
  loop : -2.53 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 135 
 TYR   0.024   0.002   TYR C 507 
 PHE   0.013   0.002   PHE C 714 
 TRP   0.022   0.001   TRP A 551 
 HIS   0.007   0.001   HIS D  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6172)
  covalent geometry    : angle       0.81141 ( 8363)
  SS BOND              : bond        0.00539 (   15)
  SS BOND              : angle       1.32249 (   30)
  hydrogen bonds       : bond        0.03610 (  101)
  hydrogen bonds       : angle       6.96069 (  258)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 137
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8083 (mm-30)
REVERT: A   83 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7124 (mtp180)
REVERT: A  125 LEU cc_start: 0.8183 (mt) cc_final: 0.7902 (mt)
REVERT: A  239 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8212 (mm-30)
REVERT: A  265 LYS cc_start: 0.8209 (tppt) cc_final: 0.7589 (tmtt)
REVERT: A  313 HIS cc_start: 0.2739 (OUTLIER) cc_final: 0.2262 (t-90)
REVERT: A  357 ASN cc_start: 0.7737 (t0) cc_final: 0.7472 (t0)
REVERT: A  383 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7942 (mtm110)
REVERT: A  411 LEU cc_start: 0.8460 (mm) cc_final: 0.8160 (mp)
REVERT: A  465 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7219 (mp10)
REVERT: A  500 LEU cc_start: 0.7864 (pp) cc_final: 0.7643 (tt)
REVERT: A  560 THR cc_start: 0.3561 (OUTLIER) cc_final: 0.3082 (p)
REVERT: C  484 LYS cc_start: 0.8246 (mptt) cc_final: 0.7921 (mmtt)
REVERT: C  504 MET cc_start: 0.6813 (mpp) cc_final: 0.6264 (mpp)
REVERT: C  551 TRP cc_start: 0.7478 (t-100) cc_final: 0.7228 (t-100)
REVERT: C  559 TRP cc_start: 0.0542 (OUTLIER) cc_final: -0.3168 (m-10)
REVERT: C  587 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.5608 (m-80)
REVERT: C  695 GLU cc_start: 0.8441 (pm20) cc_final: 0.8216 (pm20)
REVERT: D   76 ASN cc_start: 0.6319 (m-40) cc_final: 0.5929 (m-40)
  outliers start: 32
  outliers final: 22
  residues processed: 160
  average time/residue: 0.0811
  time to fit residues: 16.6367
Evaluate side-chains
  159 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  251 TRP
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  465 GLN
Chi-restraints excluded: chain A residue  474 LYS
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  507 TYR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  591 ASP
Chi-restraints excluded: chain C residue  559 TRP
Chi-restraints excluded: chain C residue  568 THR
Chi-restraints excluded: chain C residue  570 VAL
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  587 TYR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   27 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0170
   chunk 64 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 31 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A  15 ASN
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** 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 = 0.4433 r_free = 0.4433 target = 0.170606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.151353 restraints weight = 16134.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.155992 restraints weight = 9907.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.158830 restraints weight = 5852.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.159859 restraints weight = 4122.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.161446 restraints weight = 3306.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6242
moved from start:          0.5382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6187  Z= 0.133
  Angle     :  0.831  10.833   8393  Z= 0.395
  Chirality :  0.049   0.228    905
  Planarity :  0.005   0.070   1070
  Dihedral  :  5.769  22.624    805
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.01 %
    Favored  : 89.99 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 31.71 %
    Favored  : 64.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.10 (0.30), residues: 719
  helix: -1.84 (0.51), residues: 94
  sheet: -1.02 (0.60), residues: 79
  loop : -2.47 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 135 
 TYR   0.028   0.002   TYR A 277 
 PHE   0.014   0.002   PHE C 714 
 TRP   0.025   0.001   TRP A 551 
 HIS   0.007   0.001   HIS D  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6172)
  covalent geometry    : angle       0.82922 ( 8363)
  SS BOND              : bond        0.00483 (   15)
  SS BOND              : angle       1.31186 (   30)
  hydrogen bonds       : bond        0.03499 (  101)
  hydrogen bonds       : angle       6.93046 (  258)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 140
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8057 (mm-30)
REVERT: A   83 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7066 (mtp180)
REVERT: A  189 GLN cc_start: 0.5856 (OUTLIER) cc_final: 0.5485 (mt0)
REVERT: A  239 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8210 (mm-30)
REVERT: A  265 LYS cc_start: 0.8233 (tppt) cc_final: 0.7602 (tmtt)
REVERT: A  313 HIS cc_start: 0.2527 (OUTLIER) cc_final: 0.1996 (t-90)
REVERT: A  357 ASN cc_start: 0.7824 (t0) cc_final: 0.7478 (t0)
REVERT: A  383 ARG cc_start: 0.8337 (mtt180) cc_final: 0.7945 (mtm110)
REVERT: A  411 LEU cc_start: 0.8330 (mm) cc_final: 0.8050 (mp)
REVERT: A  465 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7240 (mp10)
REVERT: A  553 MET cc_start: 0.7656 (mmt) cc_final: 0.7209 (mmm)
REVERT: A  560 THR cc_start: 0.3505 (OUTLIER) cc_final: 0.3091 (p)
REVERT: C  484 LYS cc_start: 0.8179 (mptt) cc_final: 0.7812 (mmtt)
REVERT: C  504 MET cc_start: 0.6977 (mpp) cc_final: 0.6672 (mpp)
REVERT: C  551 TRP cc_start: 0.7396 (t-100) cc_final: 0.7149 (t-100)
REVERT: C  559 TRP cc_start: 0.0576 (OUTLIER) cc_final: -0.3155 (m-10)
REVERT: C  587 TYR cc_start: 0.6537 (OUTLIER) cc_final: 0.5588 (m-80)
REVERT: C  695 GLU cc_start: 0.8495 (pm20) cc_final: 0.8241 (pm20)
  outliers start: 29
  outliers final: 20
  residues processed: 159
  average time/residue: 0.0773
  time to fit residues: 15.9523
Evaluate side-chains
  161 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  189 GLN
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  251 TRP
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  465 GLN
Chi-restraints excluded: chain A residue  474 LYS
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  507 TYR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  591 ASP
Chi-restraints excluded: chain C residue  559 TRP
Chi-restraints excluded: chain C residue  568 THR
Chi-restraints excluded: chain C residue  570 VAL
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  579 TYR
Chi-restraints excluded: chain C residue  587 TYR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   27 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 1 optimal weight:    0.0170
   chunk 41 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.5822

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 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 = 0.4380 r_free = 0.4380 target = 0.166223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.146611 restraints weight = 15958.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.150975 restraints weight = 10032.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.154490 restraints weight = 6101.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.155035 restraints weight = 4048.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.156289 restraints weight = 3476.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.4270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6368
moved from start:          0.5201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6187  Z= 0.168
  Angle     :  0.866  12.031   8393  Z= 0.425
  Chirality :  0.051   0.253    905
  Planarity :  0.005   0.072   1070
  Dihedral  :  6.032  31.038    805
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 18.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.10 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 32.60 %
    Favored  : 62.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.19 (0.30), residues: 719
  helix: -1.90 (0.50), residues: 93
  sheet: -1.27 (0.60), residues: 80
  loop : -2.50 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 135 
 TYR   0.028   0.002   TYR C 507 
 PHE   0.016   0.002   PHE A  39 
 TRP   0.063   0.002   TRP A 551 
 HIS   0.007   0.001   HIS D  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 6172)
  covalent geometry    : angle       0.86418 ( 8363)
  SS BOND              : bond        0.00482 (   15)
  SS BOND              : angle       1.30594 (   30)
  hydrogen bonds       : bond        0.03810 (  101)
  hydrogen bonds       : angle       7.29744 (  258)

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

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

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1438 Ramachandran restraints generated.
    719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 140
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8104 (mm-30)
REVERT: A   83 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6981 (mtp180)
REVERT: A  148 ASN cc_start: 0.8134 (t0) cc_final: 0.7622 (p0)
REVERT: A  189 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.6251 (mt0)
REVERT: A  265 LYS cc_start: 0.8305 (tppt) cc_final: 0.7745 (tmtt)
REVERT: A  313 HIS cc_start: 0.2818 (OUTLIER) cc_final: 0.2230 (t-90)
REVERT: A  383 ARG cc_start: 0.8427 (mtt180) cc_final: 0.8048 (mtm110)
REVERT: A  411 LEU cc_start: 0.8340 (mm) cc_final: 0.7972 (mp)
REVERT: A  465 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7365 (mp10)
REVERT: C  504 MET cc_start: 0.6781 (mpp) cc_final: 0.6531 (mpp)
REVERT: C  551 TRP cc_start: 0.7767 (t-100) cc_final: 0.7520 (t-100)
REVERT: C  559 TRP cc_start: 0.0752 (OUTLIER) cc_final: -0.2876 (m-10)
REVERT: C  587 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.5748 (m-80)
REVERT: C  695 GLU cc_start: 0.8518 (pm20) cc_final: 0.8292 (pm20)
REVERT: D   25 PHE cc_start: 0.7424 (m-80) cc_final: 0.7144 (m-80)
  outliers start: 30
  outliers final: 22
  residues processed: 160
  average time/residue: 0.0821
  time to fit residues: 16.8522
Evaluate side-chains
  162 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  189 GLN
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  251 TRP
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  313 HIS
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  437 SER
Chi-restraints excluded: chain A residue  465 GLN
Chi-restraints excluded: chain A residue  474 LYS
Chi-restraints excluded: chain A residue  478 ILE
Chi-restraints excluded: chain A residue  507 TYR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  548 HIS
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain C residue  559 TRP
Chi-restraints excluded: chain C residue  568 THR
Chi-restraints excluded: chain C residue  570 VAL
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  579 TYR
Chi-restraints excluded: chain C residue  587 TYR
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   27 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0970
   chunk 48 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 30 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0570
   chunk 55 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   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  15 ASN
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 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 = 0.4421 r_free = 0.4421 target = 0.169570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.150290 restraints weight = 16180.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.154788 restraints weight = 10001.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.157714 restraints weight = 6000.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.158724 restraints weight = 4177.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.160282 restraints weight = 3389.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6279
moved from start:          0.5420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6187  Z= 0.138
  Angle     :  0.872  14.279   8393  Z= 0.415
  Chirality :  0.050   0.233    905
  Planarity :  0.005   0.066   1070
  Dihedral  :  5.872  23.641    805
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 16.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.29 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 32.60 %
    Favored  : 63.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.11 (0.30), residues: 719
  helix: -1.88 (0.50), residues: 95
  sheet: -1.18 (0.60), residues: 80
  loop : -2.44 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  86 
 TYR   0.025   0.002   TYR A 277 
 PHE   0.023   0.002   PHE A  39 
 TRP   0.013   0.001   TRP A 551 
 HIS   0.005   0.001   HIS D  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6172)
  covalent geometry    : angle       0.87212 ( 8363)
  SS BOND              : bond        0.00433 (   15)
  SS BOND              : angle       0.95483 (   30)
  hydrogen bonds       : bond        0.03694 (  101)
  hydrogen bonds       : angle       7.16950 (  258)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1160.78 seconds
wall clock time: 20 minutes 43.64 seconds (1243.64 seconds total)