Starting phenix.real_space_refine
on Thu Jul 24 20:21:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7li8_23363/07_2025/7li8_23363.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7li8_23363/07_2025/7li8_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_23363/07_2025/7li8_23363.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7li8_23363/07_2025/7li8_23363.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7li8_23363/07_2025/7li8_23363.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7li8_23363/07_2025/7li8_23363.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.21, per 1000 atoms: 0.84
  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: 1.72
  Conformation dependent library (CDL) restraints added in 906.3 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: 0.65
  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: 1.69

  Time building geometry restraints manager: 2.02 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:                  0.010
  Normalize map: mean=0, sd=1:             4.110
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.700
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.080
-------------------------------------------------------------------------------
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 : 6.92
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.012   0.000   TRP A 204 
 HIS   0.001   0.000   HIS A 223 
 PHE   0.013   0.000   PHE B 125 
 TYR   0.011   0.001   TYR A 175 
 ARG   0.001   0.000   ARG A 298 

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

*********************** 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  : 0.706 
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: 0.2157
  time to fit residues: 41.8826
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  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 19 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.4077 r_free = 0.4077 target = 0.154069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.119939 restraints weight = 10121.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.123940 restraints weight = 6353.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.126687 restraints weight = 4715.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6355  Z= 0.209
  Angle     :  0.654   9.750   8608  Z= 0.327
  Chirality :  0.042   0.228    942
  Planarity :  0.004   0.032   1047
  Dihedral  :  5.017  57.905    946
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 12.29 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.30), residues: 761
  helix: -0.35 (0.26), residues: 353
  sheet: -2.64 (0.50), residues: 92
  loop : -2.11 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 271 
 HIS   0.004   0.001   HIS C 100 
 PHE   0.032   0.002   PHE A 287 
 TYR   0.024   0.002   TYR A 358 
 ARG   0.006   0.001   ARG B  59 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00611 (    1)
  link_NAG-ASN         : angle       1.26961 (    3)
  link_BETA1-4         : bond        0.00287 (    1)
  link_BETA1-4         : angle       0.50651 (    3)
  hydrogen bonds       : bond        0.03760 (  265)
  hydrogen bonds       : angle       4.44157 (  756)
  SS BOND              : bond        0.00563 (    3)
  SS BOND              : angle       2.94306 (    6)
  covalent geometry    : bond        0.00496 ( 6349)
  covalent geometry    : angle       0.64964 ( 8596)
  Misc. bond           : bond        0.00070 (    1)

*********************** 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
  145 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.6020 (mmpt) cc_final: 0.5201 (ptmt)
REVERT: A  145 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7818 (t0)
REVERT: A  548 PHE cc_start: 0.7924 (m-80) cc_final: 0.7660 (t80)
REVERT: A  592 TYR cc_start: 0.8678 (t80) cc_final: 0.8423 (t80)
REVERT: B   53 MET cc_start: 0.7443 (ttm) cc_final: 0.7196 (ttm)
REVERT: C  110 TYR cc_start: 0.7913 (m-80) cc_final: 0.7700 (m-80)
  outliers start: 23
  outliers final: 19
  residues processed: 135
  average time/residue: 0.1909
  time to fit residues: 34.2127
Evaluate side-chains
  126 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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  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  378 VAL
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  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   37 VAL
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4067 r_free = 0.4067 target = 0.152536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.118083 restraints weight = 10381.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.122005 restraints weight = 6692.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.124643 restraints weight = 5052.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6355  Z= 0.151
  Angle     :  0.597   9.317   8608  Z= 0.297
  Chirality :  0.041   0.236    942
  Planarity :  0.004   0.032   1047
  Dihedral  :  4.931  57.430    946
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 16.64 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.31), residues: 761
  helix:  0.17 (0.27), residues: 352
  sheet: -1.83 (0.56), residues: 87
  loop : -2.00 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 204 
 HIS   0.003   0.001   HIS A 223 
 PHE   0.019   0.001   PHE A 377 
 TYR   0.040   0.002   TYR A 358 
 ARG   0.006   0.001   ARG C  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00234 (    1)
  link_NAG-ASN         : angle       1.33571 (    3)
  link_BETA1-4         : bond        0.00130 (    1)
  link_BETA1-4         : angle       0.60106 (    3)
  hydrogen bonds       : bond        0.03054 (  265)
  hydrogen bonds       : angle       4.20786 (  756)
  SS BOND              : bond        0.00409 (    3)
  SS BOND              : angle       2.18220 (    6)
  covalent geometry    : bond        0.00360 ( 6349)
  covalent geometry    : angle       0.59373 ( 8596)
  Misc. bond           : bond        0.00054 (    1)

*********************** 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
  147 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.6017 (mmpt) cc_final: 0.5147 (ptmt)
REVERT: A  260 MET cc_start: 0.7762 (tmm) cc_final: 0.7369 (tmt)
REVERT: A  538 ARG cc_start: 0.8658 (mtp180) cc_final: 0.8443 (mtm110)
REVERT: A  548 PHE cc_start: 0.7979 (m-80) cc_final: 0.7704 (t80)
REVERT: A  592 TYR cc_start: 0.8690 (t80) cc_final: 0.8459 (t80)
REVERT: B   53 MET cc_start: 0.7521 (ttm) cc_final: 0.7305 (ttm)
REVERT: C  110 TYR cc_start: 0.7880 (m-80) cc_final: 0.7435 (m-10)
  outliers start: 30
  outliers final: 22
  residues processed: 137
  average time/residue: 0.1815
  time to fit residues: 33.4090
Evaluate side-chains
  125 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
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  383 LEU
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  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   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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0970
   chunk 65 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0970
   chunk 15 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.148102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.116799 restraints weight = 10248.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.120376 restraints weight = 6810.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.122831 restraints weight = 5226.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.3240

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= 0.111
  Angle     :  0.570   9.480   8608  Z= 0.282
  Chirality :  0.040   0.242    942
  Planarity :  0.003   0.031   1047
  Dihedral  :  4.783  58.714    946
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.13 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.31), residues: 761
  helix:  0.38 (0.28), residues: 352
  sheet: -1.66 (0.56), residues: 85
  loop : -1.91 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 151 
 HIS   0.002   0.000   HIS A 223 
 PHE   0.020   0.001   PHE A 377 
 TYR   0.029   0.001   TYR B 120 
 ARG   0.004   0.000   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00379 (    1)
  link_NAG-ASN         : angle       1.43817 (    3)
  link_BETA1-4         : bond        0.00413 (    1)
  link_BETA1-4         : angle       0.81058 (    3)
  hydrogen bonds       : bond        0.02647 (  265)
  hydrogen bonds       : angle       4.04274 (  756)
  SS BOND              : bond        0.00101 (    3)
  SS BOND              : angle       1.80121 (    6)
  covalent geometry    : bond        0.00263 ( 6349)
  covalent geometry    : angle       0.56768 ( 8596)
  Misc. bond           : bond        0.00037 (    1)

*********************** 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
  136 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5960 (mmpt) cc_final: 0.5110 (ptmt)
REVERT: A  260 MET cc_start: 0.7703 (tmm) cc_final: 0.7331 (tmt)
REVERT: A  385 TYR cc_start: 0.7321 (t80) cc_final: 0.6951 (t80)
REVERT: A  548 PHE cc_start: 0.7923 (m-80) cc_final: 0.7714 (t80)
REVERT: C  110 TYR cc_start: 0.7827 (m-80) cc_final: 0.7439 (m-10)
  outliers start: 20
  outliers final: 16
  residues processed: 132
  average time/residue: 0.2445
  time to fit residues: 44.0250
Evaluate side-chains
  121 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
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  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  446 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 21 optimal weight:    0.3980
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 111 GLN
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.159485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.132578 restraints weight = 9133.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.134559 restraints weight = 6962.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.136309 restraints weight = 5813.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6355  Z= 0.164
  Angle     :  0.615   9.384   8608  Z= 0.306
  Chirality :  0.041   0.238    942
  Planarity :  0.004   0.032   1047
  Dihedral  :  5.055  57.935    946
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 17.73 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.31), residues: 761
  helix:  0.49 (0.28), residues: 352
  sheet: -1.57 (0.54), residues: 86
  loop : -1.95 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 204 
 HIS   0.004   0.001   HIS A 223 
 PHE   0.022   0.001   PHE A 377 
 TYR   0.028   0.002   TYR B 120 
 ARG   0.002   0.000   ARG A 152 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00359 (    1)
  link_NAG-ASN         : angle       1.38839 (    3)
  link_BETA1-4         : bond        0.00554 (    1)
  link_BETA1-4         : angle       0.92586 (    3)
  hydrogen bonds       : bond        0.02999 (  265)
  hydrogen bonds       : angle       4.19107 (  756)
  SS BOND              : bond        0.00511 (    3)
  SS BOND              : angle       2.20236 (    6)
  covalent geometry    : bond        0.00396 ( 6349)
  covalent geometry    : angle       0.61199 ( 8596)
  Misc. bond           : bond        0.00002 (    1)

*********************** 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
  144 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5432 (mmpt) cc_final: 0.4833 (ptmt)
REVERT: A  260 MET cc_start: 0.7928 (tmm) cc_final: 0.7655 (tmt)
REVERT: C   71 LEU cc_start: 0.8637 (tp) cc_final: 0.8344 (tt)
  outliers start: 31
  outliers final: 26
  residues processed: 134
  average time/residue: 0.2375
  time to fit residues: 45.2538
Evaluate side-chains
  127 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
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  421 THR
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  512 VAL
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  566 PHE
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   23 VAL
Chi-restraints excluded: chain C residue   96 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0870
   chunk 69 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 0 optimal weight:   30.0000
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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**
** 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 = 0.4014 r_free = 0.4014 target = 0.160349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.133364 restraints weight = 9218.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.135740 restraints weight = 7027.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.137392 restraints weight = 5855.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.3778

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= 0.120
  Angle     :  0.600   9.807   8608  Z= 0.296
  Chirality :  0.041   0.240    942
  Planarity :  0.003   0.032   1047
  Dihedral  :  4.922  58.306    946
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 21.15 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.31), residues: 761
  helix:  0.65 (0.28), residues: 351
  sheet: -1.40 (0.56), residues: 86
  loop : -1.84 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 204 
 HIS   0.003   0.001   HIS A 223 
 PHE   0.021   0.001   PHE A 377 
 TYR   0.042   0.002   TYR A 358 
 ARG   0.002   0.000   ARG A 462 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00412 (    1)
  link_NAG-ASN         : angle       1.45209 (    3)
  link_BETA1-4         : bond        0.00444 (    1)
  link_BETA1-4         : angle       0.84484 (    3)
  hydrogen bonds       : bond        0.02669 (  265)
  hydrogen bonds       : angle       3.99993 (  756)
  SS BOND              : bond        0.00299 (    3)
  SS BOND              : angle       1.83211 (    6)
  covalent geometry    : bond        0.00284 ( 6349)
  covalent geometry    : angle       0.59751 ( 8596)
  Misc. bond           : bond        0.00017 (    1)

*********************** 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
  139 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5519 (mmpt) cc_final: 0.4905 (ptmt)
REVERT: A  260 MET cc_start: 0.7848 (tmm) cc_final: 0.7612 (tmt)
REVERT: A  464 ARG cc_start: 0.7272 (mmp80) cc_final: 0.5124 (tpp-160)
REVERT: A  548 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.5969 (t80)
REVERT: C   71 LEU cc_start: 0.8611 (tp) cc_final: 0.8321 (tt)
  outliers start: 27
  outliers final: 22
  residues processed: 132
  average time/residue: 0.2604
  time to fit residues: 47.1147
Evaluate side-chains
  126 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
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  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  503 THR
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain C residue   96 SER
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 68 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 19 optimal weight:    0.3980
   chunk 45 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 72 optimal weight:    6.9990
   chunk 5 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.167654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.141120 restraints weight = 8916.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.143578 restraints weight = 6626.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.144967 restraints weight = 5404.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3979

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= 0.148
  Angle     :  0.641  10.282   8608  Z= 0.314
  Chirality :  0.042   0.239    942
  Planarity :  0.004   0.031   1047
  Dihedral  :  5.009  57.745    946
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 22.71 %
    Favored  : 73.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.31), residues: 761
  helix:  0.62 (0.28), residues: 352
  sheet: -1.43 (0.56), residues: 87
  loop : -1.80 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 204 
 HIS   0.003   0.001   HIS A 223 
 PHE   0.022   0.001   PHE A 377 
 TYR   0.024   0.002   TYR A 385 
 ARG   0.005   0.000   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00318 (    1)
  link_NAG-ASN         : angle       1.34560 (    3)
  link_BETA1-4         : bond        0.00486 (    1)
  link_BETA1-4         : angle       0.84969 (    3)
  hydrogen bonds       : bond        0.02832 (  265)
  hydrogen bonds       : angle       4.09279 (  756)
  SS BOND              : bond        0.00187 (    3)
  SS BOND              : angle       2.19581 (    6)
  covalent geometry    : bond        0.00362 ( 6349)
  covalent geometry    : angle       0.63860 ( 8596)
  Misc. bond           : bond        0.00006 (    1)

*********************** 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
  142 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5405 (mmpt) cc_final: 0.4876 (ptmt)
REVERT: A  260 MET cc_start: 0.7886 (tmm) cc_final: 0.7676 (tmt)
REVERT: A  464 ARG cc_start: 0.7302 (mmp80) cc_final: 0.5236 (tpp-160)
REVERT: A  548 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6108 (t80)
REVERT: B   47 ARG cc_start: 0.7118 (mtm180) cc_final: 0.6829 (mtm-85)
REVERT: C   71 LEU cc_start: 0.8636 (tp) cc_final: 0.8357 (tt)
  outliers start: 26
  outliers final: 24
  residues processed: 133
  average time/residue: 0.2937
  time to fit residues: 52.3356
Evaluate side-chains
  135 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 1.589 
-------------------------------------------------------------------------------
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  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  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  503 THR
Chi-restraints excluded: chain A residue  548 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 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 53 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 70 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 52 optimal weight:    6.9990
   chunk 11 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   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**
** C  62 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 = 0.4043 r_free = 0.4043 target = 0.163478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.136395 restraints weight = 8935.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.138799 restraints weight = 6765.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.140111 restraints weight = 5610.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   6355  Z= 0.154
  Angle     :  0.658  10.802   8608  Z= 0.322
  Chirality :  0.042   0.237    942
  Planarity :  0.004   0.031   1047
  Dihedral  :  5.039  58.041    946
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 22.40 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.31), residues: 761
  helix:  0.67 (0.28), residues: 346
  sheet: -1.32 (0.56), residues: 87
  loop : -1.75 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 204 
 HIS   0.002   0.001   HIS A 223 
 PHE   0.022   0.001   PHE A 377 
 TYR   0.028   0.002   TYR B 120 
 ARG   0.006   0.000   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00332 (    1)
  link_NAG-ASN         : angle       1.37654 (    3)
  link_BETA1-4         : bond        0.00467 (    1)
  link_BETA1-4         : angle       0.89484 (    3)
  hydrogen bonds       : bond        0.02847 (  265)
  hydrogen bonds       : angle       4.12397 (  756)
  SS BOND              : bond        0.00566 (    3)
  SS BOND              : angle       2.17053 (    6)
  covalent geometry    : bond        0.00380 ( 6349)
  covalent geometry    : angle       0.65558 ( 8596)
  Misc. bond           : bond        0.00006 (    1)

*********************** 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
  143 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5427 (mmpt) cc_final: 0.4854 (ptmt)
REVERT: A  260 MET cc_start: 0.7923 (tmm) cc_final: 0.7722 (tmt)
REVERT: A  464 ARG cc_start: 0.7272 (mmp80) cc_final: 0.5241 (tpp-160)
REVERT: A  548 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.6165 (t80)
REVERT: C   71 LEU cc_start: 0.8628 (tp) cc_final: 0.8350 (tt)
  outliers start: 31
  outliers final: 28
  residues processed: 132
  average time/residue: 0.2958
  time to fit residues: 52.0856
Evaluate side-chains
  138 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
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  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  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   24 GLN
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  134 THR
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 53 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 57 optimal weight:    0.3980
   chunk 64 optimal weight:    0.6980
   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**
** 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 = 0.4087 r_free = 0.4087 target = 0.167298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.141182 restraints weight = 8877.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.143705 restraints weight = 6570.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.145480 restraints weight = 5329.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6355  Z= 0.132
  Angle     :  0.659  11.660   8608  Z= 0.319
  Chirality :  0.042   0.243    942
  Planarity :  0.004   0.056   1047
  Dihedral  :  4.982  57.741    946
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 22.71 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.31), residues: 761
  helix:  0.72 (0.28), residues: 351
  sheet: -1.20 (0.54), residues: 98
  loop : -1.74 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 204 
 HIS   0.001   0.000   HIS A 223 
 PHE   0.022   0.001   PHE A 377 
 TYR   0.024   0.001   TYR A 385 
 ARG   0.015   0.001   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00341 (    1)
  link_NAG-ASN         : angle       1.28402 (    3)
  link_BETA1-4         : bond        0.00444 (    1)
  link_BETA1-4         : angle       0.82741 (    3)
  hydrogen bonds       : bond        0.02699 (  265)
  hydrogen bonds       : angle       4.08855 (  756)
  SS BOND              : bond        0.00110 (    3)
  SS BOND              : angle       1.95126 (    6)
  covalent geometry    : bond        0.00323 ( 6349)
  covalent geometry    : angle       0.65669 ( 8596)
  Misc. bond           : bond        0.00006 (    1)

*********************** 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
  137 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 1.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5377 (mmpt) cc_final: 0.4825 (ptmt)
REVERT: A  260 MET cc_start: 0.7897 (tmm) cc_final: 0.7683 (tmt)
REVERT: A  464 ARG cc_start: 0.7216 (mmp80) cc_final: 0.5228 (tpp-160)
REVERT: A  548 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6205 (t80)
REVERT: C   71 LEU cc_start: 0.8617 (tp) cc_final: 0.8317 (tt)
  outliers start: 27
  outliers final: 25
  residues processed: 128
  average time/residue: 0.4933
  time to fit residues: 85.6114
Evaluate side-chains
  133 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
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  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  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   24 GLN
Chi-restraints excluded: chain B residue  134 THR
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 33 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 71 optimal weight:    0.3980
   chunk 63 optimal weight:    0.0980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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**
** 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 = 0.4054 r_free = 0.4054 target = 0.164351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.137935 restraints weight = 9068.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.140318 restraints weight = 6816.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.141697 restraints weight = 5615.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.4170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6355  Z= 0.123
  Angle     :  0.673  12.092   8608  Z= 0.322
  Chirality :  0.042   0.243    942
  Planarity :  0.003   0.032   1047
  Dihedral  :  4.866  57.770    946
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 22.71 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.32), residues: 761
  helix:  0.81 (0.28), residues: 350
  sheet: -1.28 (0.52), residues: 99
  loop : -1.73 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 204 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.025   0.001   PHE A 586 
 TYR   0.025   0.001   TYR A 385 
 ARG   0.004   0.000   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00339 (    1)
  link_NAG-ASN         : angle       1.30881 (    3)
  link_BETA1-4         : bond        0.00403 (    1)
  link_BETA1-4         : angle       0.81127 (    3)
  hydrogen bonds       : bond        0.02588 (  265)
  hydrogen bonds       : angle       4.02859 (  756)
  SS BOND              : bond        0.00174 (    3)
  SS BOND              : angle       1.91177 (    6)
  covalent geometry    : bond        0.00300 ( 6349)
  covalent geometry    : angle       0.67144 ( 8596)
  Misc. bond           : bond        0.00015 (    1)

********************** 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
  136 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LYS cc_start: 0.5396 (mmpt) cc_final: 0.4851 (ptmt)
REVERT: A  260 MET cc_start: 0.7894 (tmm) cc_final: 0.7685 (tmt)
REVERT: A  464 ARG cc_start: 0.7139 (mmp80) cc_final: 0.5239 (tpp80)
REVERT: B   82 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7294 (mtmt)
REVERT: C   71 LEU cc_start: 0.8568 (tp) cc_final: 0.8298 (tt)
  outliers start: 25
  outliers final: 22
  residues processed: 129
  average time/residue: 0.2311
  time to fit residues: 40.6971
Evaluate side-chains
  127 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
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  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  600 THR
Chi-restraints excluded: chain A residue  604 PHE
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue  134 THR
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 47 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0270
   chunk 16 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 61 optimal weight:    0.4980
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** 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 = 0.4111 r_free = 0.4111 target = 0.169345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.142709 restraints weight = 8950.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.145182 restraints weight = 6635.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.146936 restraints weight = 5398.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6355  Z= 0.127
  Angle     :  0.671  12.027   8608  Z= 0.324
  Chirality :  0.041   0.251    942
  Planarity :  0.004   0.031   1047
  Dihedral  :  4.828  57.761    946
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 22.71 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.31), residues: 761
  helix:  0.85 (0.28), residues: 351
  sheet: -1.27 (0.54), residues: 88
  loop : -1.71 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 204 
 HIS   0.001   0.000   HIS A 235 
 PHE   0.021   0.001   PHE A 377 
 TYR   0.041   0.002   TYR A 358 
 ARG   0.003   0.000   ARG B  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00327 (    1)
  link_NAG-ASN         : angle       1.30632 (    3)
  link_BETA1-4         : bond        0.00428 (    1)
  link_BETA1-4         : angle       0.83411 (    3)
  hydrogen bonds       : bond        0.02575 (  265)
  hydrogen bonds       : angle       3.98997 (  756)
  SS BOND              : bond        0.00173 (    3)
  SS BOND              : angle       1.86693 (    6)
  covalent geometry    : bond        0.00308 ( 6349)
  covalent geometry    : angle       0.66907 ( 8596)
  Misc. bond           : bond        0.00016 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3804.59 seconds
wall clock time: 70 minutes 14.17 seconds (4214.17 seconds total)