Starting phenix.real_space_refine
on Tue Mar  3 15:30:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7li8_23363/03_2026/7li8_23363.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7li8_23363/03_2026/7li8_23363.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7li8_23363/03_2026/7li8_23363.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7li8_23363/03_2026/7li8_23363.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7li8_23363/03_2026/7li8_23363.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7li8_23363/03_2026/7li8_23363.cif"
  }
  resolution = 3.9
  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=   0.025
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      34      5.16       5
     C    4104      2.51       5
     N     962      2.21       5
     O    1081      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  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: 6181
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 539, 4303
          Classifications: {'peptide': 539}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 515}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 912
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 912
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "C"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 829
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 109
          Unusual residues: {'D10': 1, 'D12': 3, 'HP6': 6, 'LNK': 1, 'R16': 1}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 1.39, per 1000 atoms: 0.22
  Number of scatterers: 6181
  At special positions: 0
  Unit cell: (68.688, 77.112, 122.472, 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      34     16.00
     O    1081      8.00
     N     962      7.00
     C    4104      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 112 " 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=1, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 208 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 272.2 milliseconds
  

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1400

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      51.0% alpha, 9.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 98 through 103
    Processing helix  chain 'A' and resid 103 through 112
      removed outlier: 3.679A  pdb=" N   TYR A 107 " --> pdb=" O   TRP A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 129
    Processing helix  chain 'A' and resid 129 through 143
    Processing helix  chain 'A' and resid 148 through 153
    Processing helix  chain 'A' and resid 159 through 176
      removed outlier: 4.107A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 190
      removed outlier: 4.028A  pdb=" N   MET A 180 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 252 through 268
      removed outlier: 3.628A  pdb=" N   CYS A 258 " --> pdb=" O   GLN A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 286
      removed outlier: 3.769A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 301
      removed outlier: 4.317A  pdb=" N   SER A 293 " --> pdb=" O   TYR A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 313
    Processing helix  chain 'A' and resid 316 through 320
    Processing helix  chain 'A' and resid 325 through 338
      removed outlier: 3.660A  pdb=" N   GLY A 338 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 349
    Processing helix  chain 'A' and resid 359 through 389
      removed outlier: 3.988A  pdb=" N   VAL A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   TYR A 385 " --> pdb=" O   THR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 397
      removed outlier: 3.802A  pdb=" N   VAL A 397 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 415
      removed outlier: 4.411A  pdb=" N   PHE A 407 " --> pdb=" O   PRO A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 448
      removed outlier: 4.117A  pdb=" N   ALA A 441 " --> pdb=" O   ASP A 437 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU A 443 " --> pdb=" O   THR A 439 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY A 445 " --> pdb=" O   ALA A 441 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   VAL A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR A 448 " --> pdb=" O   GLU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 477
    Processing helix  chain 'A' and resid 478 through 482
      removed outlier: 3.842A  pdb=" N   THR A 482 " --> pdb=" O   VAL A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 496
      removed outlier: 4.382A  pdb=" N   LEU A 491 " --> pdb=" O   TYR A 487 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLU A 494 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA A 496 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 515
      removed outlier: 3.769A  pdb=" N   LEU A 502 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 530
    Processing helix  chain 'A' and resid 534 through 558
      removed outlier: 3.641A  pdb=" N   ARG A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   TRP A 541 " --> pdb=" O   TRP A 537 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   VAL A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA A 543 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
      removed outlier: 5.707A  pdb=" N   SER A 545 " --> pdb=" O   TRP A 541 " (cutoff:3.500A)
      Proline residue:  A 546  - end of helix
    Processing helix  chain 'A' and resid 571 through 585
      removed outlier: 4.187A  pdb=" N   ILE A 575 " --> pdb=" O   PRO A 571 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE A 576 " --> pdb=" O   TYR A 572 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   SER A 585 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 598
      removed outlier: 3.813A  pdb=" N   ILE A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 613
      removed outlier: 3.743A  pdb=" N   THR A 613 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 51
      removed outlier: 4.165A  pdb=" N   TYR B  50 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   SER B  51 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 47 through 51'
    Processing helix  chain 'C' and resid 103 through 107
      removed outlier: 3.519A  pdb=" N   THR C 107 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565
    Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 25
      removed outlier: 3.633A  pdb=" N   GLN B  24 " --> pdb=" O   LYS B  42 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LYS B  42 " --> pdb=" O   GLN B  24 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE B  39 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   MET B 100 " --> pdb=" O   ILE B  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79
      removed outlier: 3.526A  pdb=" N   ILE B  67 " --> pdb=" O   TRP B  55 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79
      removed outlier: 3.526A  pdb=" N   ILE B  67 " --> pdb=" O   TRP B  55 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31
    Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78
      removed outlier: 3.774A  pdb=" N   TYR C  73 " --> pdb=" O   ASN C  77 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   TRP C  59 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   TYR C  73 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   LEU C  57 " --> pdb=" O   TYR C  73 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78
      removed outlier: 3.774A  pdb=" N   TYR C  73 " --> pdb=" O   ASN C  77 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   TRP C  59 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   TYR C  73 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   LEU C  57 " --> pdb=" O   TYR C  73 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 90
      removed outlier: 3.561A  pdb=" N   SER C  89 " --> pdb=" O   SER C  96 " (cutoff:3.500A)

    273 hydrogen bonds defined for protein.
    756 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: 0.97

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1811
        1.34 -     1.46: 1452
        1.46 -     1.58: 3037
        1.58 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 6349
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.35e+00
  bond pdb=" C2  NAG D   1 "
       pdb=" N2  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.439  1.464 -0.025 2.00e-02 2.50e+03 1.56e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.430 -0.024 2.00e-02 2.50e+03 1.50e+00
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.33e+00
  bond pdb=" C5  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.24e+00
  ... (remaining 6344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 8193
        1.08 -     2.16: 247
        2.16 -     3.24: 65
        3.24 -     4.32: 79
        4.32 -     5.40: 12
  Bond angle restraints: 8596
  Sorted by residual:
  angle pdb=" N   VAL A 102 "
        pdb=" CA  VAL A 102 "
        pdb=" C   VAL A 102 "
      ideal   model   delta    sigma   weight residual
     113.53  109.27    4.26 9.80e-01 1.04e+00 1.89e+01
  angle pdb=" N   VAL A  92 "
        pdb=" CA  VAL A  92 "
        pdb=" C   VAL A  92 "
      ideal   model   delta    sigma   weight residual
     113.71  110.54    3.17 9.50e-01 1.11e+00 1.11e+01
  angle pdb=" N   VAL A 446 "
        pdb=" CA  VAL A 446 "
        pdb=" C   VAL A 446 "
      ideal   model   delta    sigma   weight residual
     112.96  109.70    3.26 1.00e+00 1.00e+00 1.07e+01
  angle pdb=" C   GLY B 121 "
        pdb=" N   SER B 122 "
        pdb=" CA  SER B 122 "
      ideal   model   delta    sigma   weight residual
     120.38  124.54   -4.16 1.37e+00 5.33e-01 9.22e+00
  angle pdb=" C   MET B 127 "
        pdb=" N   ASP B 128 "
        pdb=" CA  ASP B 128 "
      ideal   model   delta    sigma   weight residual
     121.54  126.14   -4.60 1.91e+00 2.74e-01 5.79e+00
  ... (remaining 8591 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.73: 3326
       14.73 -    29.46: 272
       29.46 -    44.19: 59
       44.19 -    58.91: 9
       58.91 -    73.64: 2
  Dihedral angle restraints: 3668
    sinusoidal: 1462
      harmonic: 2206
  Sorted by residual:
  dihedral pdb=" CB  CYS B  41 "
           pdb=" SG  CYS B  41 "
           pdb=" SG  CYS B 115 "
           pdb=" CB  CYS B 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.64  -73.64     1      1.00e+01 1.00e-02 6.90e+01
  dihedral pdb=" CA  TRP A 204 "
           pdb=" C   TRP A 204 "
           pdb=" N   ASN A 205 "
           pdb=" CA  ASN A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.98   22.02     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  ASP A  87 "
           pdb=" CB  ASP A  87 "
           pdb=" CG  ASP A  87 "
           pdb=" OD1 ASP A  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.66   52.66     1      2.00e+01 2.50e-03 9.44e+00
  ... (remaining 3665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 929
       0.103 -    0.206: 12
       0.206 -    0.309: 0
       0.309 -    0.413: 0
       0.413 -    0.516: 1
  Chirality restraints: 942
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.88   -0.52 2.00e-02 2.50e+03 6.65e+02
  chirality pdb=" C2  NAG D   1 "
            pdb=" C1  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" N2  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.32   -0.17 2.00e-01 2.50e+01 7.05e-01
  chirality pdb=" CB  THR C 107 "
            pdb=" CA  THR C 107 "
            pdb=" OG1 THR C 107 "
            pdb=" CG2 THR C 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 939 not shown)

  Planarity restraints: 1048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 338 "   -0.022 5.00e-02 4.00e+02   3.30e-02 1.74e+00
        pdb=" N   PRO A 339 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 339 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 339 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 130 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.33e+00
        pdb=" N   PRO A 131 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 131 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 131 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 128 "   -0.005 2.00e-02 2.50e+03   1.07e-02 1.15e+00
        pdb=" C   ASP B 128 "    0.019 2.00e-02 2.50e+03
        pdb=" O   ASP B 128 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   TYR B 129 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1045 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1068
        2.76 -     3.30: 5736
        3.30 -     3.83: 9932
        3.83 -     4.37: 10836
        4.37 -     4.90: 19149
  Nonbonded interactions: 46721
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 110 "
            pdb=" O   VAL A 394 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER B  49 "
            pdb=" O   PRO B  72 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   LYS A 201 "
            pdb=" NE1 TRP B  52 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   SER A 477 "
            pdb=" OG  SER A 477 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OG  SER B  36 "
            pdb=" O   LEU B 102 "
     model   vdw
     2.330 3.040
  ... (remaining 46716 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:             5.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.930
  Find NCS groups from input model:        0.030
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
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      :  0.002   0.065   6355  Z= 0.117
  Angle     :  0.636  14.044   8608  Z= 0.308
  Chirality :  0.041   0.516    942
  Planarity :  0.003   0.033   1047
  Dihedral  : 10.905  69.682   2259
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.23 (0.27), residues: 761
  helix: -1.23 (0.23), residues: 353
  sheet: -2.94 (0.51), residues: 82
  loop : -2.92 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 298 
 TYR   0.011   0.001   TYR A 175 
 PHE   0.013   0.000   PHE B 125 
 TRP   0.012   0.000   TRP A 204 
 HIS   0.001   0.000   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 6349)
  covalent geometry    : angle       0.60121 ( 8596)
  SS BOND              : bond        0.00070 (    3)
  SS BOND              : angle       0.24147 (    6)
  hydrogen bonds       : bond        0.18544 (  265)
  hydrogen bonds       : angle       5.83901 (  756)
  Misc. bond           : bond        0.00023 (    1)
  link_BETA1-4         : bond        0.06516 (    1)
  link_BETA1-4         : angle      11.10597 (    3)
  link_NAG-ASN         : bond        0.00293 (    1)
  link_NAG-ASN         : angle       1.61201 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.6008 (mmpt) cc_final: 0.5241 (ptmt)
REVERT: A  152 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8428 (mmt90)
REVERT: A  222 LEU cc_start: 0.7905 (tp) cc_final: 0.7315 (tp)
REVERT: B   58 GLN cc_start: 0.8476 (tt0) cc_final: 0.8096 (tt0)
REVERT: C   62 GLN cc_start: 0.8044 (tt0) cc_final: 0.7838 (tt0)
REVERT: C  110 TYR cc_start: 0.7845 (m-80) cc_final: 0.7568 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0936
  time to fit residues: 18.1310
Evaluate side-chains
  117 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0570
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.9704

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 194 GLN
A 354 ASN
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.158976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.124830 restraints weight = 10152.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.129242 restraints weight = 6170.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.132289 restraints weight = 4487.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.133913 restraints weight = 3630.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.135304 restraints weight = 3193.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6355  Z= 0.146
  Angle     :  0.597   9.552   8608  Z= 0.295
  Chirality :  0.041   0.238    942
  Planarity :  0.004   0.032   1047
  Dihedral  :  4.806  58.394    946
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 12.75 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.31), residues: 761
  helix: -0.16 (0.27), residues: 350
  sheet: -2.39 (0.53), residues: 86
  loop : -2.01 (0.37), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 523 
 TYR   0.028   0.002   TYR A 358 
 PHE   0.025   0.001   PHE A 287 
 TRP   0.011   0.001   TRP B  55 
 HIS   0.002   0.001   HIS C 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6349)
  covalent geometry    : angle       0.59348 ( 8596)
  SS BOND              : bond        0.00865 (    3)
  SS BOND              : angle       2.34057 (    6)
  hydrogen bonds       : bond        0.03055 (  265)
  hydrogen bonds       : angle       4.25525 (  756)
  Misc. bond           : bond        0.00071 (    1)
  link_BETA1-4         : bond        0.00413 (    1)
  link_BETA1-4         : angle       0.91648 (    3)
  link_NAG-ASN         : bond        0.00429 (    1)
  link_NAG-ASN         : angle       1.58154 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5943 (mmpt) cc_final: 0.5174 (ptmt)
REVERT: A  222 LEU cc_start: 0.7874 (tp) cc_final: 0.7622 (tp)
REVERT: A  548 PHE cc_start: 0.7785 (m-80) cc_final: 0.7573 (t80)
REVERT: A  592 TYR cc_start: 0.8657 (t80) cc_final: 0.8396 (t80)
REVERT: B   53 MET cc_start: 0.7411 (ttm) cc_final: 0.7178 (ttm)
REVERT: B   58 GLN cc_start: 0.8529 (tt0) cc_final: 0.8144 (tt0)
REVERT: C   62 GLN cc_start: 0.8307 (tt0) cc_final: 0.8092 (tt0)
REVERT: C  110 TYR cc_start: 0.7789 (m-80) cc_final: 0.7524 (m-80)
REVERT: C  116 LYS cc_start: 0.5472 (mttp) cc_final: 0.3573 (ttmt)
  outliers start: 21
  outliers final: 16
  residues processed: 138
  average time/residue: 0.0731
  time to fit residues: 13.4030
Evaluate side-chains
  124 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 50 optimal weight:    0.6980
   chunk 61 optimal weight:    9.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 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 = 0.4118 r_free = 0.4118 target = 0.157024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.122579 restraints weight = 10240.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.126756 restraints weight = 6350.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.129579 restraints weight = 4690.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.131471 restraints weight = 3837.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.132489 restraints weight = 3372.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6355  Z= 0.132
  Angle     :  0.571   9.389   8608  Z= 0.283
  Chirality :  0.040   0.243    942
  Planarity :  0.004   0.040   1047
  Dihedral  :  4.670  57.660    946
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 15.71 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.31), residues: 761
  helix:  0.26 (0.28), residues: 351
  sheet: -1.93 (0.55), residues: 86
  loop : -1.96 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  85 
 TYR   0.016   0.001   TYR B 120 
 PHE   0.019   0.001   PHE A 377 
 TRP   0.010   0.001   TRP A 271 
 HIS   0.002   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6349)
  covalent geometry    : angle       0.56843 ( 8596)
  SS BOND              : bond        0.00312 (    3)
  SS BOND              : angle       1.84499 (    6)
  hydrogen bonds       : bond        0.02838 (  265)
  hydrogen bonds       : angle       4.07676 (  756)
  Misc. bond           : bond        0.00026 (    1)
  link_BETA1-4         : bond        0.00641 (    1)
  link_BETA1-4         : angle       0.79838 (    3)
  link_NAG-ASN         : bond        0.00258 (    1)
  link_NAG-ASN         : angle       1.43109 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.6033 (mmpt) cc_final: 0.5195 (ptmt)
REVERT: A  260 MET cc_start: 0.7627 (tmm) cc_final: 0.7275 (tmt)
REVERT: A  548 PHE cc_start: 0.7797 (m-80) cc_final: 0.7596 (t80)
REVERT: A  592 TYR cc_start: 0.8634 (t80) cc_final: 0.8434 (t80)
REVERT: C  110 TYR cc_start: 0.7793 (m-80) cc_final: 0.7585 (m-80)
  outliers start: 24
  outliers final: 19
  residues processed: 134
  average time/residue: 0.0723
  time to fit residues: 13.0963
Evaluate side-chains
  123 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:   30.0000
   chunk 37 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 12 optimal weight:    0.2980
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 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 = 0.4026 r_free = 0.4026 target = 0.149480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.114337 restraints weight = 10674.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.118214 restraints weight = 6928.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.120831 restraints weight = 5241.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.122600 restraints weight = 4374.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.123533 restraints weight = 3875.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.3621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   6355  Z= 0.195
  Angle     :  0.646   9.380   8608  Z= 0.326
  Chirality :  0.043   0.234    942
  Planarity :  0.004   0.034   1047
  Dihedral  :  5.323  58.217    946
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 18.66 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.31), residues: 761
  helix:  0.27 (0.28), residues: 350
  sheet: -1.72 (0.56), residues: 86
  loop : -1.87 (0.36), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 538 
 TYR   0.043   0.002   TYR A 358 
 PHE   0.023   0.002   PHE A 586 
 TRP   0.024   0.002   TRP A 204 
 HIS   0.002   0.001   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 6349)
  covalent geometry    : angle       0.64191 ( 8596)
  SS BOND              : bond        0.00547 (    3)
  SS BOND              : angle       2.51002 (    6)
  hydrogen bonds       : bond        0.03346 (  265)
  hydrogen bonds       : angle       4.34804 (  756)
  Misc. bond           : bond        0.00007 (    1)
  link_BETA1-4         : bond        0.00320 (    1)
  link_BETA1-4         : angle       0.86953 (    3)
  link_NAG-ASN         : bond        0.00250 (    1)
  link_NAG-ASN         : angle       1.39717 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5961 (mmpt) cc_final: 0.5049 (ptmt)
REVERT: A  260 MET cc_start: 0.7892 (tmm) cc_final: 0.7490 (tmt)
REVERT: A  548 PHE cc_start: 0.8017 (m-80) cc_final: 0.7758 (t80)
REVERT: B   53 MET cc_start: 0.7352 (ttm) cc_final: 0.7013 (ttm)
REVERT: C  105 ASP cc_start: 0.7965 (t0) cc_final: 0.7763 (t0)
REVERT: C  110 TYR cc_start: 0.8088 (m-80) cc_final: 0.7490 (m-10)
  outliers start: 30
  outliers final: 24
  residues processed: 136
  average time/residue: 0.0724
  time to fit residues: 13.2343
Evaluate side-chains
  132 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 31 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 51 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 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 = 0.3882 r_free = 0.3882 target = 0.146972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.114878 restraints weight = 10120.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.118562 restraints weight = 6740.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.121047 restraints weight = 5129.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.122367 restraints weight = 4285.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.123759 restraints weight = 3832.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6355  Z= 0.124
  Angle     :  0.597   9.437   8608  Z= 0.295
  Chirality :  0.041   0.241    942
  Planarity :  0.003   0.032   1047
  Dihedral  :  4.981  58.101    946
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 20.53 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.31), residues: 761
  helix:  0.51 (0.28), residues: 352
  sheet: -1.51 (0.56), residues: 86
  loop : -1.86 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 464 
 TYR   0.030   0.001   TYR B 120 
 PHE   0.024   0.001   PHE A 586 
 TRP   0.014   0.001   TRP A 204 
 HIS   0.004   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6349)
  covalent geometry    : angle       0.59429 ( 8596)
  SS BOND              : bond        0.00905 (    3)
  SS BOND              : angle       1.90375 (    6)
  hydrogen bonds       : bond        0.02683 (  265)
  hydrogen bonds       : angle       4.02540 (  756)
  Misc. bond           : bond        0.00018 (    1)
  link_BETA1-4         : bond        0.00591 (    1)
  link_BETA1-4         : angle       0.89513 (    3)
  link_NAG-ASN         : bond        0.00336 (    1)
  link_NAG-ASN         : angle       1.39657 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5922 (mmpt) cc_final: 0.5054 (ptmt)
REVERT: A  260 MET cc_start: 0.7771 (tmm) cc_final: 0.7377 (tmt)
REVERT: A  548 PHE cc_start: 0.7958 (m-80) cc_final: 0.7747 (t80)
REVERT: C  110 TYR cc_start: 0.7922 (m-80) cc_final: 0.7405 (m-10)
  outliers start: 28
  outliers final: 23
  residues processed: 131
  average time/residue: 0.0681
  time to fit residues: 12.0615
Evaluate side-chains
  127 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 62 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.157706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.130334 restraints weight = 9207.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.132493 restraints weight = 7044.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.133774 restraints weight = 5875.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.135065 restraints weight = 5236.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.135540 restraints weight = 4776.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077   6355  Z= 0.186
  Angle     :  0.654   9.687   8608  Z= 0.326
  Chirality :  0.042   0.232    942
  Planarity :  0.004   0.033   1047
  Dihedral  :  5.297  57.326    946
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 21.00 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.31), residues: 761
  helix:  0.48 (0.28), residues: 351
  sheet: -1.44 (0.57), residues: 86
  loop : -1.82 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  44 
 TYR   0.025   0.002   TYR B 120 
 PHE   0.022   0.001   PHE A 377 
 TRP   0.023   0.001   TRP A 204 
 HIS   0.002   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 6349)
  covalent geometry    : angle       0.65177 ( 8596)
  SS BOND              : bond        0.00460 (    3)
  SS BOND              : angle       2.16823 (    6)
  hydrogen bonds       : bond        0.03176 (  265)
  hydrogen bonds       : angle       4.23869 (  756)
  Misc. bond           : bond        0.00012 (    1)
  link_BETA1-4         : bond        0.00438 (    1)
  link_BETA1-4         : angle       0.84851 (    3)
  link_NAG-ASN         : bond        0.00291 (    1)
  link_NAG-ASN         : angle       1.27571 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5465 (mmpt) cc_final: 0.4864 (ptmt)
REVERT: A  260 MET cc_start: 0.7974 (tmm) cc_final: 0.7741 (tmt)
  outliers start: 32
  outliers final: 26
  residues processed: 135
  average time/residue: 0.0726
  time to fit residues: 13.2815
Evaluate side-chains
  134 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.162101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.134974 restraints weight = 9012.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.137291 restraints weight = 6868.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.138748 restraints weight = 5705.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.139957 restraints weight = 5032.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.140412 restraints weight = 4589.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6355  Z= 0.132
  Angle     :  0.632  10.023   8608  Z= 0.311
  Chirality :  0.041   0.228    942
  Planarity :  0.003   0.033   1047
  Dihedral  :  5.131  57.786    946
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 21.31 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.32), residues: 761
  helix:  0.64 (0.28), residues: 351
  sheet: -1.38 (0.54), residues: 97
  loop : -1.76 (0.37), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  44 
 TYR   0.026   0.001   TYR B 120 
 PHE   0.022   0.001   PHE A 377 
 TRP   0.018   0.001   TRP C  59 
 HIS   0.003   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6349)
  covalent geometry    : angle       0.62956 ( 8596)
  SS BOND              : bond        0.00588 (    3)
  SS BOND              : angle       2.02368 (    6)
  hydrogen bonds       : bond        0.02760 (  265)
  hydrogen bonds       : angle       4.03572 (  756)
  Misc. bond           : bond        0.00009 (    1)
  link_BETA1-4         : bond        0.00398 (    1)
  link_BETA1-4         : angle       0.82491 (    3)
  link_NAG-ASN         : bond        0.00352 (    1)
  link_NAG-ASN         : angle       1.21980 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5415 (mmpt) cc_final: 0.4828 (ptmt)
REVERT: A  260 MET cc_start: 0.7882 (tmm) cc_final: 0.7671 (tmt)
REVERT: A  464 ARG cc_start: 0.7274 (mmp80) cc_final: 0.5105 (tpp-160)
REVERT: B   47 ARG cc_start: 0.7132 (mtm180) cc_final: 0.6850 (mtm-85)
REVERT: C   71 LEU cc_start: 0.8626 (tp) cc_final: 0.8264 (tt)
  outliers start: 30
  outliers final: 28
  residues processed: 135
  average time/residue: 0.0694
  time to fit residues: 12.6679
Evaluate side-chains
  138 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 24 optimal weight:    0.1980
   chunk 22 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 69 optimal weight:    0.3980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.170161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.141378 restraints weight = 9070.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.144085 restraints weight = 6568.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.145670 restraints weight = 5314.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.147091 restraints weight = 4658.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.147577 restraints weight = 4231.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.4205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6355  Z= 0.154
  Angle     :  0.672  11.309   8608  Z= 0.326
  Chirality :  0.042   0.232    942
  Planarity :  0.004   0.033   1047
  Dihedral  :  5.184  57.792    946
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 22.08 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.32), residues: 761
  helix:  0.59 (0.28), residues: 351
  sheet: -1.68 (0.55), residues: 92
  loop : -1.67 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  44 
 TYR   0.032   0.002   TYR A 358 
 PHE   0.023   0.001   PHE A 377 
 TRP   0.013   0.001   TRP A 204 
 HIS   0.002   0.001   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 6349)
  covalent geometry    : angle       0.66970 ( 8596)
  SS BOND              : bond        0.00452 (    3)
  SS BOND              : angle       2.05678 (    6)
  hydrogen bonds       : bond        0.02906 (  265)
  hydrogen bonds       : angle       4.15698 (  756)
  Misc. bond           : bond        0.00003 (    1)
  link_BETA1-4         : bond        0.00460 (    1)
  link_BETA1-4         : angle       0.82207 (    3)
  link_NAG-ASN         : bond        0.00359 (    1)
  link_NAG-ASN         : angle       1.10290 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5631 (mmpt) cc_final: 0.4916 (ptmt)
REVERT: A  260 MET cc_start: 0.7946 (tmm) cc_final: 0.7705 (tmt)
REVERT: A  464 ARG cc_start: 0.7297 (mmp80) cc_final: 0.5134 (tpp-160)
REVERT: A  548 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6258 (t80)
  outliers start: 31
  outliers final: 28
  residues processed: 138
  average time/residue: 0.0756
  time to fit residues: 14.0274
Evaluate side-chains
  141 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 52 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.170884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.142889 restraints weight = 8961.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.145384 restraints weight = 6691.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.146995 restraints weight = 5502.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.147861 restraints weight = 4813.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.148775 restraints weight = 4459.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6355  Z= 0.143
  Angle     :  0.677  11.793   8608  Z= 0.331
  Chirality :  0.042   0.245    942
  Planarity :  0.004   0.033   1047
  Dihedral  :  5.099  57.738    946
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 23.02 %
    Favored  : 72.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.31), residues: 761
  helix:  0.66 (0.28), residues: 351
  sheet: -1.52 (0.53), residues: 103
  loop : -1.67 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  44 
 TYR   0.038   0.002   TYR A 358 
 PHE   0.022   0.001   PHE A 377 
 TRP   0.011   0.001   TRP A 204 
 HIS   0.001   0.000   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6349)
  covalent geometry    : angle       0.67553 ( 8596)
  SS BOND              : bond        0.00268 (    3)
  SS BOND              : angle       1.68176 (    6)
  hydrogen bonds       : bond        0.02831 (  265)
  hydrogen bonds       : angle       4.07983 (  756)
  Misc. bond           : bond        0.00002 (    1)
  link_BETA1-4         : bond        0.00389 (    1)
  link_BETA1-4         : angle       0.83062 (    3)
  link_NAG-ASN         : bond        0.00370 (    1)
  link_NAG-ASN         : angle       1.20256 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5579 (mmpt) cc_final: 0.4909 (ptmt)
REVERT: A  103 TRP cc_start: 0.7549 (t60) cc_final: 0.7342 (t60)
REVERT: A  464 ARG cc_start: 0.7260 (mmp80) cc_final: 0.5252 (tpp80)
REVERT: A  548 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6289 (t80)
REVERT: B   82 LYS cc_start: 0.8347 (mmtm) cc_final: 0.7339 (mtmt)
  outliers start: 31
  outliers final: 29
  residues processed: 135
  average time/residue: 0.0788
  time to fit residues: 14.3710
Evaluate side-chains
  140 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 11 optimal weight:    0.0970
   chunk 20 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    0.4980
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 31 optimal weight:    0.2980
   chunk 67 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.169761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.144020 restraints weight = 8863.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.145405 restraints weight = 7343.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.146044 restraints weight = 6234.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.146399 restraints weight = 5558.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.146685 restraints weight = 5182.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.4292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6355  Z= 0.125
  Angle     :  0.689  12.187   8608  Z= 0.332
  Chirality :  0.042   0.240    942
  Planarity :  0.004   0.041   1047
  Dihedral  :  5.003  58.496    946
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 24.26 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.31), residues: 761
  helix:  0.74 (0.28), residues: 351
  sheet: -1.11 (0.57), residues: 86
  loop : -1.77 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  47 
 TYR   0.038   0.002   TYR A 358 
 PHE   0.021   0.001   PHE A 377 
 TRP   0.011   0.001   TRP A 204 
 HIS   0.002   0.000   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6349)
  covalent geometry    : angle       0.68742 ( 8596)
  SS BOND              : bond        0.00308 (    3)
  SS BOND              : angle       1.73231 (    6)
  hydrogen bonds       : bond        0.02605 (  265)
  hydrogen bonds       : angle       4.00223 (  756)
  Misc. bond           : bond        0.00015 (    1)
  link_BETA1-4         : bond        0.00434 (    1)
  link_BETA1-4         : angle       0.90773 (    3)
  link_NAG-ASN         : bond        0.00502 (    1)
  link_NAG-ASN         : angle       1.30781 (    3)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5069 (mmpt) cc_final: 0.4735 (ptmt)
REVERT: A  410 TYR cc_start: 0.7050 (m-80) cc_final: 0.6826 (m-80)
REVERT: A  464 ARG cc_start: 0.7204 (mmp80) cc_final: 0.5220 (tpp80)
REVERT: A  548 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.6272 (t80)
REVERT: B   82 LYS cc_start: 0.8303 (mmtm) cc_final: 0.7344 (mtmt)
  outliers start: 24
  outliers final: 22
  residues processed: 131
  average time/residue: 0.0832
  time to fit residues: 14.4643
Evaluate side-chains
  135 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  204 TRP
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  446 VAL
Chi-restraints excluded: chain A residue  457 VAL
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  104 GLU
Chi-restraints excluded: chain C residue  126 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 5 optimal weight:    0.4980
   chunk 58 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 28 optimal weight:    0.2980
   chunk 27 optimal weight:    7.9990
   chunk 67 optimal weight:    0.7980
   chunk 1 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0020
   chunk 54 optimal weight:    0.0170
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.3226

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

Flipped N/Q/H residues before XYZ refinement:
A 211 ASN
** B  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.173885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.147468 restraints weight = 8617.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.149898 restraints weight = 6311.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.151354 restraints weight = 5157.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.152826 restraints weight = 4500.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.153388 restraints weight = 4065.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.4267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6355  Z= 0.120
  Angle     :  0.684  11.996   8608  Z= 0.328
  Chirality :  0.041   0.255    942
  Planarity :  0.003   0.032   1047
  Dihedral  :  4.879  57.905    946
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 24.88 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.31), residues: 761
  helix:  0.79 (0.28), residues: 355
  sheet: -1.21 (0.56), residues: 86
  loop : -1.74 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  47 
 TYR   0.036   0.002   TYR A 358 
 PHE   0.022   0.001   PHE A 377 
 TRP   0.011   0.001   TRP A 103 
 HIS   0.002   0.000   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6349)
  covalent geometry    : angle       0.68206 ( 8596)
  SS BOND              : bond        0.00355 (    3)
  SS BOND              : angle       1.85685 (    6)
  hydrogen bonds       : bond        0.02494 (  265)
  hydrogen bonds       : angle       3.91187 (  756)
  Misc. bond           : bond        0.00028 (    1)
  link_BETA1-4         : bond        0.00452 (    1)
  link_BETA1-4         : angle       0.86431 (    3)
  link_NAG-ASN         : bond        0.00419 (    1)
  link_NAG-ASN         : angle       1.22306 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1185.56 seconds
wall clock time: 21 minutes 7.94 seconds (1267.94 seconds total)