Starting phenix.real_space_refine
on Mon Apr 28 09:56:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bgf_44511/04_2025/9bgf_44511.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bgf_44511/04_2025/9bgf_44511.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bgf_44511/04_2025/9bgf_44511.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bgf_44511/04_2025/9bgf_44511.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bgf_44511/04_2025/9bgf_44511.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bgf_44511/04_2025/9bgf_44511.cif"
  }
  resolution = 2.9
  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=   0.001
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: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     P       4      5.49       5
     Mg      4      5.21       5
     S      37      5.16       5
     C    4638      2.51       5
     N    1238      2.21       5
     O    1394      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7317
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 438, 3650
          Classifications: {'peptide': 438}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 415}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 3471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3471
          Classifications: {'peptide': 419}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 396}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 98
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 98
          Unusual residues: {' CA': 1, ' MG': 2, 'NAG': 4, 'UD1': 1}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 70
          Unusual residues: {' CA': 1, ' MG': 2, 'NAG': 2, 'UD1': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.25, per 1000 atoms: 0.72
  Number of scatterers: 7317
  At special positions: 0
  Unit cell: (72.864, 102.672, 111.78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      2     19.99
     S      37     16.00
     P       4     15.00
     Mg      4     11.99
     O    1394      8.00
     N    1238      7.00
     C    4638      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  70 " - pdb=" SG  CYS B  70 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG A1304 " - " ASN A1129 "
      " NAG A1305 " - " ASN A 376 "
      " NAG A1306 " - " ASN A  83 "
      " NAG A1307 " - " ASN A1009 "
      " NAG B1301 " - " ASN B1129 "
      " NAG B1304 " - " ASN B 376 "
      " NAG C   1 " - " ASN B  83 "
  Time building additional restraints: 1.74
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1670

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 12 sheets defined
      51.7% alpha, 13.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 56
      removed outlier: 4.233A  pdb=" N   TYR A  56 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 70
    Processing helix  chain 'A' and resid 85 through 104
      removed outlier: 3.547A  pdb=" N   GLU A 101 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU A 103 " --> pdb=" O   GLN A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 323
    Processing helix  chain 'A' and resid 327 through 340
      removed outlier: 3.584A  pdb=" N   TYR A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 373
    Processing helix  chain 'A' and resid 376 through 380
      removed outlier: 4.266A  pdb=" N   HIS A 379 " --> pdb=" O   ASN A 376 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   LEU A 380 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 376 through 380'
    Processing helix  chain 'A' and resid 384 through 390
    Processing helix  chain 'A' and resid 391 through 395
    Processing helix  chain 'A' and resid 416 through 419
    Processing helix  chain 'A' and resid 931 through 947
    Processing helix  chain 'A' and resid 963 through 973
    Processing helix  chain 'A' and resid 973 through 983
    Processing helix  chain 'A' and resid 992 through 1002
    Processing helix  chain 'A' and resid 1009 through 1018
    Processing helix  chain 'A' and resid 1026 through 1038
    Processing helix  chain 'A' and resid 1043 through 1061
    Processing helix  chain 'A' and resid 1088 through 1093
    Processing helix  chain 'A' and resid 1094 through 1105
    Processing helix  chain 'A' and resid 1129 through 1143
      removed outlier: 3.606A  pdb=" N   GLY A1135 " --> pdb=" O   SER A1131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1159 through 1176
      removed outlier: 4.582A  pdb=" N   THR A1163 " --> pdb=" O   LYS A1159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1194 through 1203
    Processing helix  chain 'B' and resid 50 through 55
    Processing helix  chain 'B' and resid 56 through 58
      No H-bonds generated for 'chain 'B' and resid 56 through 58'
    Processing helix  chain 'B' and resid 65 through 70
    Processing helix  chain 'B' and resid 85 through 98
      removed outlier: 4.015A  pdb=" N   LEU B  90 " --> pdb=" O   ASP B  86 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LYS B  91 " --> pdb=" O   LEU B  87 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLN B  95 " --> pdb=" O   LYS B  91 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG B  97 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLU B  98 " --> pdb=" O   GLN B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 340
      removed outlier: 3.597A  pdb=" N   TYR B 331 " --> pdb=" O   GLU B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 374
    Processing helix  chain 'B' and resid 376 through 380
      removed outlier: 3.616A  pdb=" N   HIS B 379 " --> pdb=" O   ASN B 376 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LEU B 380 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 376 through 380'
    Processing helix  chain 'B' and resid 384 through 391
      removed outlier: 3.919A  pdb=" N   HIS B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 395
      removed outlier: 4.143A  pdb=" N   ILE B 395 " --> pdb=" O   ILE B 392 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 392 through 395'
    Processing helix  chain 'B' and resid 416 through 419
    Processing helix  chain 'B' and resid 931 through 947
    Processing helix  chain 'B' and resid 963 through 973
    Processing helix  chain 'B' and resid 973 through 983
    Processing helix  chain 'B' and resid 992 through 1002
    Processing helix  chain 'B' and resid 1009 through 1018
    Processing helix  chain 'B' and resid 1026 through 1038
    Processing helix  chain 'B' and resid 1043 through 1060
    Processing helix  chain 'B' and resid 1088 through 1093
    Processing helix  chain 'B' and resid 1094 through 1105
    Processing helix  chain 'B' and resid 1129 through 1143
    Processing helix  chain 'B' and resid 1159 through 1176
      removed outlier: 4.197A  pdb=" N   THR B1163 " --> pdb=" O   LYS B1159 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 368
      removed outlier: 6.467A  pdb=" N   ILE A 346 " --> pdb=" O   THR A 366 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   VAL A 368 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   ILE A 348 " --> pdb=" O   VAL A 368 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ASP A  76 " --> pdb=" O   ILE A 403 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   LEU A 405 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A 405 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 411
      removed outlier: 6.342A  pdb=" N   ALA A1122 " --> pdb=" O   CYS A1149 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   ASN A1151 " --> pdb=" O   ALA A1122 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LYS A1124 " --> pdb=" O   ASN A1151 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 421 through 422
      removed outlier: 6.703A  pdb=" N   VAL A 953 " --> pdb=" O   THR A 432 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 421 through 422
      removed outlier: 6.502A  pdb=" N   GLN A 427 " --> pdb=" O   GLU A1114 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   MET A1116 " --> pdb=" O   GLN A 427 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   VAL A 429 " --> pdb=" O   MET A1116 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1005 through 1006
      removed outlier: 4.524A  pdb=" N   LYS A1108 " --> pdb=" O   GLN A1006 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1024 through 1025
      removed outlier: 4.596A  pdb=" N   VAL A1086 " --> pdb=" O   LEU A1025 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 365 through 369
      removed outlier: 6.626A  pdb=" N   ILE B 346 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   VAL B 368 " --> pdb=" O   ILE B 346 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   ILE B 348 " --> pdb=" O   VAL B 368 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ASP B  76 " --> pdb=" O   ILE B 403 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   LEU B 405 " --> pdb=" O   ASP B  76 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   VAL B  78 " --> pdb=" O   LEU B 405 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 409 through 411
    Processing sheet with id=AA9, first strand: chain 'B' and resid 421 through 422
      removed outlier: 4.814A  pdb=" N   TRP B 433 " --> pdb=" O   VAL B 953 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 421 through 422
      removed outlier: 6.589A  pdb=" N   GLN B 427 " --> pdb=" O   GLU B1114 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   MET B1116 " --> pdb=" O   GLN B 427 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   VAL B 429 " --> pdb=" O   MET B1116 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 1005 through 1006
      removed outlier: 4.556A  pdb=" N   LYS B1108 " --> pdb=" O   GLN B1006 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 1024 through 1025
      removed outlier: 4.566A  pdb=" N   VAL B1086 " --> pdb=" O   LEU B1025 " (cutoff:3.500A)

    298 hydrogen bonds defined for protein.
    852 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: 2.27

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1558
        1.33 -     1.45: 1762
        1.45 -     1.57: 4099
        1.57 -     1.69: 8
        1.69 -     1.81: 66
  Bond restraints: 7493
  Sorted by residual:
  bond pdb=" N   THR B1128 "
       pdb=" CA  THR B1128 "
    ideal  model  delta    sigma   weight residual
    1.460  1.475 -0.015 1.54e-02 4.22e+03 9.87e-01
  bond pdb=" CA  TRP A 416 "
       pdb=" C   TRP A 416 "
    ideal  model  delta    sigma   weight residual
    1.519  1.529 -0.009 9.50e-03 1.11e+04 9.86e-01
  bond pdb=" C   TRP A 416 "
       pdb=" O   TRP A 416 "
    ideal  model  delta    sigma   weight residual
    1.236  1.227  0.009 8.90e-03 1.26e+04 9.21e-01
  bond pdb=" C1  NAG A1305 "
       pdb=" C2  NAG A1305 "
    ideal  model  delta    sigma   weight residual
    1.532  1.549 -0.017 2.00e-02 2.50e+03 7.07e-01
  bond pdb=" CA  PHE A 982 "
       pdb=" CB  PHE A 982 "
    ideal  model  delta    sigma   weight residual
    1.532  1.546 -0.014 1.78e-02 3.16e+03 5.99e-01
  ... (remaining 7488 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 9988
        1.61 -     3.23: 134
        3.23 -     4.84: 23
        4.84 -     6.46: 4
        6.46 -     8.07: 1
  Bond angle restraints: 10150
  Sorted by residual:
  angle pdb=" C1  NAG A1305 "
        pdb=" O5  NAG A1305 "
        pdb=" C5  NAG A1305 "
      ideal   model   delta    sigma   weight residual
     113.21  121.28   -8.07 3.00e+00 1.11e-01 7.24e+00
  angle pdb=" C   ARG A1127 "
        pdb=" N   THR A1128 "
        pdb=" CA  THR A1128 "
      ideal   model   delta    sigma   weight residual
     121.54  126.23   -4.69 1.91e+00 2.74e-01 6.02e+00
  angle pdb=" C   SER B 319 "
        pdb=" N   ALA B 320 "
        pdb=" CA  ALA B 320 "
      ideal   model   delta    sigma   weight residual
     121.54  126.00   -4.46 1.91e+00 2.74e-01 5.45e+00
  angle pdb=" C   PHE B 998 "
        pdb=" N   TYR B 999 "
        pdb=" CA  TYR B 999 "
      ideal   model   delta    sigma   weight residual
     122.38  118.18    4.20 1.81e+00 3.05e-01 5.38e+00
  angle pdb=" N   THR A1128 "
        pdb=" CA  THR A1128 "
        pdb=" C   THR A1128 "
      ideal   model   delta    sigma   weight residual
     110.80  115.33   -4.53 2.13e+00 2.20e-01 4.52e+00
  ... (remaining 10145 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.94: 4342
       18.94 -    37.89: 258
       37.89 -    56.83: 70
       56.83 -    75.78: 18
       75.78 -    94.72: 12
  Dihedral angle restraints: 4700
    sinusoidal: 2148
      harmonic: 2552
  Sorted by residual:
  dihedral pdb=" CA  VAL A 349 "
           pdb=" C   VAL A 349 "
           pdb=" N   THR A 350 "
           pdb=" CA  THR A 350 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.49  -20.51     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  TYR A 999 "
           pdb=" C   TYR A 999 "
           pdb=" N   TYR A1000 "
           pdb=" CA  TYR A1000 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.97   19.03     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  TYR B 999 "
           pdb=" C   TYR B 999 "
           pdb=" N   TYR B1000 "
           pdb=" CA  TYR B1000 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.44   18.56     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 4697 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 631
       0.027 -    0.054: 301
       0.054 -    0.082: 96
       0.082 -    0.109: 62
       0.109 -    0.136: 29
  Chirality restraints: 1119
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.39   -0.01 2.00e-02 2.50e+03 5.04e-01
  chirality pdb=" CA  ILE A 354 "
            pdb=" N   ILE A 354 "
            pdb=" C   ILE A 354 "
            pdb=" CB  ILE A 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  THR A1128 "
            pdb=" N   THR A1128 "
            pdb=" C   THR A1128 "
            pdb=" CB  THR A1128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.61e-01
  ... (remaining 1116 not shown)

  Planarity restraints: 1300
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  71 "    0.030 5.00e-02 4.00e+02   4.51e-02 3.25e+00
        pdb=" N   PRO A  72 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A  72 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A  72 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 982 "    0.008 2.00e-02 2.50e+03   1.02e-02 1.83e+00
        pdb=" CG  PHE A 982 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 982 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 982 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 982 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 982 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 982 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 407 "   -0.006 2.00e-02 2.50e+03   1.27e-02 1.61e+00
        pdb=" C   ASP B 407 "    0.022 2.00e-02 2.50e+03
        pdb=" O   ASP B 407 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ASP B 408 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1297 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.50: 61
        2.50 -     3.10: 5263
        3.10 -     3.70: 11426
        3.70 -     4.30: 17066
        4.30 -     4.90: 28085
  Nonbonded interactions: 61901
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B1151 "
            pdb="MG    MG B1302 "
     model   vdw
     1.906 2.170
  nonbonded pdb=" OD2 ASP B 408 "
            pdb="MG    MG B1302 "
     model   vdw
     1.946 2.170
  nonbonded pdb="MG    MG B1302 "
            pdb=" O2B UD1 B1303 "
     model   vdw
     1.951 2.170
  nonbonded pdb=" OD1 ASN A1151 "
            pdb="MG    MG A1308 "
     model   vdw
     1.981 2.170
  nonbonded pdb=" O2B UD1 A1303 "
            pdb="MG    MG A1308 "
     model   vdw
     2.026 2.170
  ... (remaining 61896 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 49 through 105 or resid 316 through 1185 or resid 1306 or  \ 
resid 1308))
  selection = (chain 'B' and (resid 49 through 1185 or resid 1304 or resid 1306))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.210
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.270
  Find NCS groups from input model:        0.300
  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:14.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
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      :  0.003   0.024   7502  Z= 0.134
  Angle     :  0.529   8.074  10176  Z= 0.268
  Chirality :  0.043   0.136   1119
  Planarity :  0.004   0.045   1293
  Dihedral  : 14.494  94.720   3027
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  5.45 %
    Favored  : 94.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  1.17 (0.30), residues: 841
  helix:  1.59 (0.28), residues: 367
  sheet:  0.74 (0.61), residues: 82
  loop :  0.09 (0.33), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  81 
 HIS   0.003   0.001   HIS B1158 
 PHE   0.023   0.002   PHE A 982 
 TYR   0.012   0.002   TYR B 937 
 ARG   0.003   0.000   ARG A 986 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00252 (    7)
  link_NAG-ASN         : angle       2.12017 (   21)
  link_BETA1-4         : bond        0.00209 (    1)
  link_BETA1-4         : angle       1.03110 (    3)
  hydrogen bonds       : bond        0.17776 (  294)
  hydrogen bonds       : angle       6.28958 (  852)
  SS BOND              : bond        0.00226 (    1)
  SS BOND              : angle       0.22266 (    2)
  covalent geometry    : bond        0.00302 ( 7493)
  covalent geometry    : angle       0.52017 (10150)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.851 
Fit side-chains
REVERT: A   94 GLN cc_start: 0.8028 (mt0) cc_final: 0.7786 (mt0)
REVERT: A 1043 SER cc_start: 0.8020 (m) cc_final: 0.7738 (p)
REVERT: A 1045 GLN cc_start: 0.7030 (mp10) cc_final: 0.6770 (mp10)
REVERT: A 1170 ASP cc_start: 0.7787 (t70) cc_final: 0.7489 (t0)
REVERT: A 1191 ARG cc_start: 0.6769 (mtm-85) cc_final: 0.4475 (mmt180)
REVERT: B   55 SER cc_start: 0.8012 (t) cc_final: 0.7720 (p)
REVERT: B  396 GLU cc_start: 0.8206 (tp30) cc_final: 0.7987 (tp30)
REVERT: B 1002 MET cc_start: 0.8596 (mtp) cc_final: 0.8383 (mtm)
REVERT: B 1016 GLU cc_start: 0.7484 (pt0) cc_final: 0.6964 (mt-10)
  outliers start: 2
  outliers final: 1
  residues processed: 118
  average time/residue: 1.4619
  time to fit residues: 181.6272
Evaluate side-chains
  98 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  407 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 25 optimal weight:    0.2980
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 406 ASN
B 326 ASN
B 362 ASN
B 967 GLN
** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1158 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.144801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.117804 restraints weight = 7490.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.25
r_work: 0.3248 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7502  Z= 0.221
  Angle     :  0.643   8.172  10176  Z= 0.330
  Chirality :  0.047   0.169   1119
  Planarity :  0.005   0.044   1293
  Dihedral  : 11.027 103.726   1214
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  :  9.79 %
    Favored  : 87.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.58 (0.29), residues: 841
  helix:  1.08 (0.27), residues: 374
  sheet:  0.66 (0.60), residues: 82
  loop : -0.28 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 416 
 HIS   0.007   0.001   HIS A 379 
 PHE   0.033   0.003   PHE A 982 
 TYR   0.014   0.002   TYR B 404 
 ARG   0.005   0.001   ARG A 986 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00259 (    7)
  link_NAG-ASN         : angle       1.99294 (   21)
  link_BETA1-4         : bond        0.00370 (    1)
  link_BETA1-4         : angle       1.04108 (    3)
  hydrogen bonds       : bond        0.05244 (  294)
  hydrogen bonds       : angle       4.85132 (  852)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       0.37333 (    2)
  covalent geometry    : bond        0.00522 ( 7493)
  covalent geometry    : angle       0.63751 (10150)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.837 
Fit side-chains
REVERT: A   91 LYS cc_start: 0.7484 (mttt) cc_final: 0.7269 (mttm)
REVERT: A 1043 SER cc_start: 0.7432 (m) cc_final: 0.6859 (p)
REVERT: A 1045 GLN cc_start: 0.7052 (mp10) cc_final: 0.6754 (mp10)
REVERT: A 1053 MET cc_start: 0.7548 (mtp) cc_final: 0.7327 (mtt)
REVERT: A 1191 ARG cc_start: 0.6804 (mtm-85) cc_final: 0.4342 (mmt180)
REVERT: B   55 SER cc_start: 0.8067 (t) cc_final: 0.7577 (p)
REVERT: B  100 MET cc_start: 0.4645 (pmm) cc_final: 0.3994 (ttp)
REVERT: B  396 GLU cc_start: 0.8325 (tp30) cc_final: 0.8116 (tp30)
REVERT: B 1016 GLU cc_start: 0.7535 (pt0) cc_final: 0.6930 (mt-10)
REVERT: B 1045 GLN cc_start: 0.7267 (mp10) cc_final: 0.6927 (mp10)
  outliers start: 20
  outliers final: 9
  residues processed: 114
  average time/residue: 1.5394
  time to fit residues: 185.8697
Evaluate side-chains
  106 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 GLU
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  976 GLU
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  408 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0370
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A  94 GLN
B 351 ASN
B1158 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.147846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.120420 restraints weight = 7539.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.29
r_work: 0.3287 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7502  Z= 0.126
  Angle     :  0.536   7.364  10176  Z= 0.274
  Chirality :  0.043   0.134   1119
  Planarity :  0.004   0.041   1293
  Dihedral  : 10.897 102.530   1214
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 11.15 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.77 (0.30), residues: 841
  helix:  1.35 (0.28), residues: 373
  sheet:  0.51 (0.59), residues: 82
  loop : -0.25 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 416 
 HIS   0.005   0.001   HIS B 987 
 PHE   0.029   0.002   PHE A 982 
 TYR   0.014   0.001   TYR B 937 
 ARG   0.002   0.000   ARG A  57 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00229 (    7)
  link_NAG-ASN         : angle       1.84566 (   21)
  link_BETA1-4         : bond        0.00452 (    1)
  link_BETA1-4         : angle       1.03584 (    3)
  hydrogen bonds       : bond        0.04112 (  294)
  hydrogen bonds       : angle       4.51851 (  852)
  SS BOND              : bond        0.00109 (    1)
  SS BOND              : angle       0.32021 (    2)
  covalent geometry    : bond        0.00284 ( 7493)
  covalent geometry    : angle       0.52979 (10150)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 1.059 
Fit side-chains
REVERT: A   91 LYS cc_start: 0.7480 (mttt) cc_final: 0.7259 (mttm)
REVERT: A  325 ASP cc_start: 0.7634 (t0) cc_final: 0.7336 (t0)
REVERT: A 1045 GLN cc_start: 0.6945 (mp10) cc_final: 0.6705 (mp10)
REVERT: A 1053 MET cc_start: 0.7532 (mtp) cc_final: 0.7324 (mtt)
REVERT: A 1191 ARG cc_start: 0.6758 (mtm-85) cc_final: 0.4269 (mmt180)
REVERT: B   55 SER cc_start: 0.8040 (t) cc_final: 0.7610 (p)
REVERT: B   94 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7200 (tm-30)
REVERT: B  100 MET cc_start: 0.4648 (pmm) cc_final: 0.3823 (ttp)
REVERT: B  396 GLU cc_start: 0.8300 (tp30) cc_final: 0.8092 (tp30)
REVERT: B  992 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7044 (tm-30)
REVERT: B 1016 GLU cc_start: 0.7572 (pt0) cc_final: 0.6929 (mt-10)
REVERT: B 1045 GLN cc_start: 0.7286 (mp10) cc_final: 0.6968 (mp-120)
  outliers start: 22
  outliers final: 9
  residues processed: 120
  average time/residue: 1.4754
  time to fit residues: 187.3517
Evaluate side-chains
  111 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASN
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  976 GLU
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  992 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.1980
   chunk 29 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0670
   chunk 1 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1158 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.148389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.120930 restraints weight = 7584.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.30
r_work: 0.3298 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7502  Z= 0.116
  Angle     :  0.528   7.492  10176  Z= 0.266
  Chirality :  0.043   0.138   1119
  Planarity :  0.004   0.038   1293
  Dihedral  : 10.803 100.900   1214
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 12.27 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.84 (0.30), residues: 841
  helix:  1.46 (0.28), residues: 373
  sheet:  0.41 (0.59), residues: 82
  loop : -0.23 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 416 
 HIS   0.005   0.001   HIS B 987 
 PHE   0.028   0.002   PHE A 982 
 TYR   0.014   0.001   TYR B 937 
 ARG   0.002   0.000   ARG A 986 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00223 (    7)
  link_NAG-ASN         : angle       1.80103 (   21)
  link_BETA1-4         : bond        0.00287 (    1)
  link_BETA1-4         : angle       1.05399 (    3)
  hydrogen bonds       : bond        0.03787 (  294)
  hydrogen bonds       : angle       4.37107 (  852)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.26403 (    2)
  covalent geometry    : bond        0.00259 ( 7493)
  covalent geometry    : angle       0.52154 (10150)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   91 LYS cc_start: 0.7433 (mttt) cc_final: 0.7197 (mttm)
REVERT: A  325 ASP cc_start: 0.7582 (t0) cc_final: 0.7299 (t0)
REVERT: A  371 GLN cc_start: 0.7775 (mm110) cc_final: 0.7499 (mp-120)
REVERT: A 1053 MET cc_start: 0.7497 (mtp) cc_final: 0.7279 (mtt)
REVERT: A 1060 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.5623 (mmm)
REVERT: A 1170 ASP cc_start: 0.7910 (t70) cc_final: 0.7547 (t0)
REVERT: A 1191 ARG cc_start: 0.6687 (mtm-85) cc_final: 0.4203 (mmt180)
REVERT: B   55 SER cc_start: 0.7988 (t) cc_final: 0.7536 (p)
REVERT: B   94 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7128 (tm-30)
REVERT: B  100 MET cc_start: 0.4807 (pmm) cc_final: 0.3288 (tmt)
REVERT: B  396 GLU cc_start: 0.8267 (tp30) cc_final: 0.8032 (tp30)
REVERT: B  992 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7067 (tm-30)
REVERT: B 1016 GLU cc_start: 0.7556 (pt0) cc_final: 0.6911 (mt-10)
REVERT: B 1045 GLN cc_start: 0.7270 (mp10) cc_final: 0.6963 (mp10)
  outliers start: 21
  outliers final: 10
  residues processed: 121
  average time/residue: 1.1928
  time to fit residues: 152.7964
Evaluate side-chains
  111 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASN
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  976 GLU
Chi-restraints excluded: chain A residue  990 ASP
Chi-restraints excluded: chain A residue 1060 MET
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  408 ASP
Chi-restraints excluded: chain B residue  992 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 71 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0270
   chunk 56 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.6240

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

Flipped N/Q/H residues before XYZ refinement:
** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1158 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.148878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.121242 restraints weight = 7457.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 1.29
r_work: 0.3296 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7502  Z= 0.128
  Angle     :  0.538   7.507  10176  Z= 0.272
  Chirality :  0.043   0.148   1119
  Planarity :  0.004   0.037   1293
  Dihedral  : 10.792 100.631   1214
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 12.14 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.81 (0.30), residues: 841
  helix:  1.46 (0.28), residues: 373
  sheet:  0.36 (0.59), residues: 82
  loop : -0.28 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 416 
 HIS   0.006   0.001   HIS B 987 
 PHE   0.028   0.002   PHE A 982 
 TYR   0.014   0.001   TYR B 937 
 ARG   0.003   0.000   ARG A 986 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00205 (    7)
  link_NAG-ASN         : angle       1.78597 (   21)
  link_BETA1-4         : bond        0.00392 (    1)
  link_BETA1-4         : angle       1.09373 (    3)
  hydrogen bonds       : bond        0.03804 (  294)
  hydrogen bonds       : angle       4.34610 (  852)
  SS BOND              : bond        0.00145 (    1)
  SS BOND              : angle       0.25678 (    2)
  covalent geometry    : bond        0.00294 ( 7493)
  covalent geometry    : angle       0.53208 (10150)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 102
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A   91 LYS cc_start: 0.7326 (mttt) cc_final: 0.7098 (mttm)
REVERT: A  325 ASP cc_start: 0.7624 (t0) cc_final: 0.7329 (t0)
REVERT: A  371 GLN cc_start: 0.7798 (mm110) cc_final: 0.7492 (mp-120)
REVERT: A 1053 MET cc_start: 0.7466 (mtp) cc_final: 0.7240 (mtt)
REVERT: A 1060 MET cc_start: 0.5829 (OUTLIER) cc_final: 0.5516 (mmm)
REVERT: A 1191 ARG cc_start: 0.6711 (mtm-85) cc_final: 0.4247 (mmt180)
REVERT: B   55 SER cc_start: 0.8003 (t) cc_final: 0.7556 (p)
REVERT: B   94 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7109 (tm-30)
REVERT: B  100 MET cc_start: 0.4899 (pmm) cc_final: 0.3497 (tmt)
REVERT: B  396 GLU cc_start: 0.8240 (tp30) cc_final: 0.8012 (tp30)
REVERT: B  414 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6808 (m-30)
REVERT: B  992 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7038 (tm-30)
REVERT: B 1016 GLU cc_start: 0.7541 (pt0) cc_final: 0.6877 (mt-10)
REVERT: B 1045 GLN cc_start: 0.7278 (mp10) cc_final: 0.6977 (mp-120)
  outliers start: 24
  outliers final: 12
  residues processed: 120
  average time/residue: 1.1732
  time to fit residues: 149.3132
Evaluate side-chains
  115 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASN
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue  976 GLU
Chi-restraints excluded: chain A residue 1060 MET
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  408 ASP
Chi-restraints excluded: chain B residue  414 ASP
Chi-restraints excluded: chain B residue  992 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   chunk 77 optimal weight:    0.4980
   chunk 15 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1158 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.147904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.120317 restraints weight = 7534.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.29
r_work: 0.3294 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7502  Z= 0.135
  Angle     :  0.546   7.445  10176  Z= 0.275
  Chirality :  0.043   0.151   1119
  Planarity :  0.004   0.035   1293
  Dihedral  : 10.826 100.961   1214
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 12.64 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.76 (0.30), residues: 841
  helix:  1.46 (0.28), residues: 374
  sheet: -0.17 (0.55), residues: 94
  loop : -0.21 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 416 
 HIS   0.006   0.001   HIS B 987 
 PHE   0.028   0.002   PHE A 982 
 TYR   0.014   0.002   TYR B 937 
 ARG   0.002   0.000   ARG A 986 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00198 (    7)
  link_NAG-ASN         : angle       1.76649 (   21)
  link_BETA1-4         : bond        0.00501 (    1)
  link_BETA1-4         : angle       1.11313 (    3)
  hydrogen bonds       : bond        0.03851 (  294)
  hydrogen bonds       : angle       4.33893 (  852)
  SS BOND              : bond        0.00115 (    1)
  SS BOND              : angle       0.28659 (    2)
  covalent geometry    : bond        0.00310 ( 7493)
  covalent geometry    : angle       0.54011 (10150)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A   91 LYS cc_start: 0.7458 (mttt) cc_final: 0.7192 (mttm)
REVERT: A  325 ASP cc_start: 0.7628 (t0) cc_final: 0.7346 (t0)
REVERT: A  371 GLN cc_start: 0.7756 (mm110) cc_final: 0.7471 (mp-120)
REVERT: A 1053 MET cc_start: 0.7491 (mtp) cc_final: 0.7272 (mtt)
REVERT: A 1060 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5787 (mmm)
REVERT: A 1191 ARG cc_start: 0.6749 (mtm-85) cc_final: 0.4264 (mmt180)
REVERT: B   55 SER cc_start: 0.8019 (t) cc_final: 0.7540 (p)
REVERT: B   94 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.7137 (tm-30)
REVERT: B  100 MET cc_start: 0.4859 (pmm) cc_final: 0.3522 (tmt)
REVERT: B  396 GLU cc_start: 0.8277 (tp30) cc_final: 0.8043 (tp30)
REVERT: B  992 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7126 (tm-30)
REVERT: B 1016 GLU cc_start: 0.7537 (pt0) cc_final: 0.6873 (mt-10)
REVERT: B 1021 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8070 (mm-40)
REVERT: B 1045 GLN cc_start: 0.7264 (mp10) cc_final: 0.6962 (mp-120)
  outliers start: 28
  outliers final: 14
  residues processed: 126
  average time/residue: 1.2425
  time to fit residues: 165.1396
Evaluate side-chains
  118 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASN
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue  976 GLU
Chi-restraints excluded: chain A residue  990 ASP
Chi-restraints excluded: chain A residue 1060 MET
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  373 VAL
Chi-restraints excluded: chain B residue  408 ASP
Chi-restraints excluded: chain B residue  992 GLN
Chi-restraints excluded: chain B residue 1021 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0980
   chunk 57 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0970
   chunk 74 optimal weight:    0.0980
   chunk 1 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0030
   overall best weight:    0.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 427 GLN
B1158 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.151824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.124577 restraints weight = 7451.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 1.30
r_work: 0.3344 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7502  Z= 0.094
  Angle     :  0.504   7.738  10176  Z= 0.253
  Chirality :  0.042   0.149   1119
  Planarity :  0.003   0.034   1293
  Dihedral  : 10.752  98.064   1214
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.88 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.98 (0.30), residues: 841
  helix:  1.67 (0.28), residues: 373
  sheet:  0.11 (0.58), residues: 84
  loop : -0.18 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 416 
 HIS   0.008   0.001   HIS B 987 
 PHE   0.027   0.001   PHE A 982 
 TYR   0.013   0.001   TYR B 937 
 ARG   0.002   0.000   ARG B  57 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00287 (    7)
  link_NAG-ASN         : angle       1.69218 (   21)
  link_BETA1-4         : bond        0.00392 (    1)
  link_BETA1-4         : angle       1.01465 (    3)
  hydrogen bonds       : bond        0.03293 (  294)
  hydrogen bonds       : angle       4.23669 (  852)
  SS BOND              : bond        0.00189 (    1)
  SS BOND              : angle       0.41667 (    2)
  covalent geometry    : bond        0.00201 ( 7493)
  covalent geometry    : angle       0.49860 (10150)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.815 
Fit side-chains
REVERT: A   91 LYS cc_start: 0.7389 (mttt) cc_final: 0.7126 (mttm)
REVERT: A  325 ASP cc_start: 0.7505 (t0) cc_final: 0.7228 (t0)
REVERT: A  371 GLN cc_start: 0.7669 (mm110) cc_final: 0.7455 (mp-120)
REVERT: A  407 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.6678 (p0)
REVERT: A 1053 MET cc_start: 0.7485 (mtp) cc_final: 0.7226 (mtt)
REVERT: A 1060 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5687 (mmm)
REVERT: A 1061 LEU cc_start: 0.4530 (OUTLIER) cc_final: 0.4029 (tp)
REVERT: A 1125 MET cc_start: 0.7925 (mmm) cc_final: 0.7685 (mpp)
REVERT: A 1191 ARG cc_start: 0.6680 (mtm-85) cc_final: 0.4187 (mmt180)
REVERT: B   55 SER cc_start: 0.7989 (t) cc_final: 0.7520 (p)
REVERT: B   94 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.7047 (tm-30)
REVERT: B  100 MET cc_start: 0.4852 (pmm) cc_final: 0.3544 (tmt)
REVERT: B  396 GLU cc_start: 0.8231 (tp30) cc_final: 0.8006 (tp30)
REVERT: B  992 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7080 (tm-30)
REVERT: B 1016 GLU cc_start: 0.7559 (pt0) cc_final: 0.6899 (mt-10)
REVERT: B 1125 MET cc_start: 0.8021 (mtp) cc_final: 0.7806 (mtp)
  outliers start: 18
  outliers final: 7
  residues processed: 120
  average time/residue: 1.1689
  time to fit residues: 148.8514
Evaluate side-chains
  112 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASN
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  976 GLU
Chi-restraints excluded: chain A residue  990 ASP
Chi-restraints excluded: chain A residue 1060 MET
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  992 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 35 optimal weight:    0.5980
   chunk 31 optimal weight:    7.9990
   chunk 79 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 427 GLN
** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1158 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.148267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.120693 restraints weight = 7561.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.29
r_work: 0.3293 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7502  Z= 0.140
  Angle     :  0.559   7.580  10176  Z= 0.283
  Chirality :  0.044   0.154   1119
  Planarity :  0.004   0.034   1293
  Dihedral  : 10.745  99.094   1214
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.24 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.89 (0.30), residues: 841
  helix:  1.59 (0.28), residues: 373
  sheet:  0.18 (0.58), residues: 84
  loop : -0.25 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 416 
 HIS   0.008   0.001   HIS B 987 
 PHE   0.028   0.002   PHE A 982 
 TYR   0.014   0.002   TYR B 937 
 ARG   0.002   0.000   ARG A 986 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00183 (    7)
  link_NAG-ASN         : angle       1.73216 (   21)
  link_BETA1-4         : bond        0.00403 (    1)
  link_BETA1-4         : angle       1.08112 (    3)
  hydrogen bonds       : bond        0.03782 (  294)
  hydrogen bonds       : angle       4.30294 (  852)
  SS BOND              : bond        0.00109 (    1)
  SS BOND              : angle       0.24029 (    2)
  covalent geometry    : bond        0.00325 ( 7493)
  covalent geometry    : angle       0.55357 (10150)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.833 
Fit side-chains
REVERT: A  325 ASP cc_start: 0.7681 (t0) cc_final: 0.7400 (t0)
REVERT: A  371 GLN cc_start: 0.7781 (mm110) cc_final: 0.7527 (mp-120)
REVERT: A  407 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7160 (p0)
REVERT: A 1053 MET cc_start: 0.7495 (mtp) cc_final: 0.7253 (mtt)
REVERT: A 1060 MET cc_start: 0.6105 (OUTLIER) cc_final: 0.5865 (mmm)
REVERT: B   55 SER cc_start: 0.8053 (t) cc_final: 0.7585 (p)
REVERT: B   94 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7079 (tm-30)
REVERT: B  396 GLU cc_start: 0.8286 (tp30) cc_final: 0.8061 (tp30)
REVERT: B  992 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7156 (tm-30)
REVERT: B 1002 MET cc_start: 0.8620 (mtp) cc_final: 0.8405 (mtm)
REVERT: B 1016 GLU cc_start: 0.7541 (pt0) cc_final: 0.6892 (mt-10)
  outliers start: 19
  outliers final: 9
  residues processed: 113
  average time/residue: 1.1281
  time to fit residues: 135.4119
Evaluate side-chains
  109 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASN
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  976 GLU
Chi-restraints excluded: chain A residue  990 ASP
Chi-restraints excluded: chain A residue 1060 MET
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  992 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 21 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0050
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1158 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.149003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.121604 restraints weight = 7533.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 1.27
r_work: 0.3322 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7502  Z= 0.126
  Angle     :  0.564   8.273  10176  Z= 0.284
  Chirality :  0.043   0.151   1119
  Planarity :  0.004   0.035   1293
  Dihedral  : 10.774  99.046   1214
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.86 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.89 (0.30), residues: 841
  helix:  1.58 (0.28), residues: 373
  sheet:  0.21 (0.58), residues: 84
  loop : -0.25 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 416 
 HIS   0.010   0.001   HIS B 987 
 PHE   0.027   0.002   PHE A 982 
 TYR   0.013   0.001   TYR B 937 
 ARG   0.002   0.000   ARG A 986 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00197 (    7)
  link_NAG-ASN         : angle       1.69970 (   21)
  link_BETA1-4         : bond        0.00413 (    1)
  link_BETA1-4         : angle       1.04846 (    3)
  hydrogen bonds       : bond        0.03649 (  294)
  hydrogen bonds       : angle       4.30667 (  852)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       0.30446 (    2)
  covalent geometry    : bond        0.00288 ( 7493)
  covalent geometry    : angle       0.55925 (10150)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.858 
Fit side-chains
REVERT: A  325 ASP cc_start: 0.7583 (t0) cc_final: 0.7310 (t0)
REVERT: A  371 GLN cc_start: 0.7730 (mm110) cc_final: 0.7490 (mp-120)
REVERT: A 1053 MET cc_start: 0.7469 (mtp) cc_final: 0.7223 (mtt)
REVERT: A 1060 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5812 (mmm)
REVERT: B   55 SER cc_start: 0.8023 (t) cc_final: 0.7556 (p)
REVERT: B   94 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.7010 (tm-30)
REVERT: B  100 MET cc_start: 0.4723 (pmm) cc_final: 0.4250 (ttp)
REVERT: B  396 GLU cc_start: 0.8258 (tp30) cc_final: 0.8037 (tp30)
REVERT: B  992 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7164 (tm-30)
REVERT: B 1016 GLU cc_start: 0.7548 (pt0) cc_final: 0.6895 (mt-10)
REVERT: B 1125 MET cc_start: 0.8031 (mtp) cc_final: 0.7759 (mtp)
  outliers start: 17
  outliers final: 11
  residues processed: 111
  average time/residue: 1.1490
  time to fit residues: 135.8050
Evaluate side-chains
  109 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASN
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  976 GLU
Chi-restraints excluded: chain A residue  990 ASP
Chi-restraints excluded: chain A residue 1060 MET
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  336 ILE
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  992 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1158 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.147945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.120556 restraints weight = 7656.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.27
r_work: 0.3297 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7502  Z= 0.145
  Angle     :  0.583   8.041  10176  Z= 0.293
  Chirality :  0.044   0.159   1119
  Planarity :  0.004   0.035   1293
  Dihedral  : 10.808  99.912   1214
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.36 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 (0.30), residues: 841
  helix:  1.53 (0.28), residues: 373
  sheet: -0.18 (0.55), residues: 94
  loop : -0.24 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 416 
 HIS   0.011   0.001   HIS B 987 
 PHE   0.028   0.002   PHE A 982 
 TYR   0.014   0.002   TYR B 331 
 ARG   0.002   0.000   ARG A 986 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00169 (    7)
  link_NAG-ASN         : angle       1.73138 (   21)
  link_BETA1-4         : bond        0.00385 (    1)
  link_BETA1-4         : angle       1.04927 (    3)
  hydrogen bonds       : bond        0.03824 (  294)
  hydrogen bonds       : angle       4.35241 (  852)
  SS BOND              : bond        0.00067 (    1)
  SS BOND              : angle       0.24849 (    2)
  covalent geometry    : bond        0.00338 ( 7493)
  covalent geometry    : angle       0.57808 (10150)

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

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

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1682 Ramachandran restraints generated.
    841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A  325 ASP cc_start: 0.7718 (t0) cc_final: 0.7464 (t0)
REVERT: A  371 GLN cc_start: 0.7724 (mm110) cc_final: 0.7485 (mp-120)
REVERT: A 1021 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8276 (mt0)
REVERT: A 1053 MET cc_start: 0.7470 (mtp) cc_final: 0.7231 (mtt)
REVERT: A 1060 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.5870 (mmm)
REVERT: B   55 SER cc_start: 0.8070 (t) cc_final: 0.7593 (p)
REVERT: B   94 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7040 (tm-30)
REVERT: B  100 MET cc_start: 0.4758 (pmm) cc_final: 0.4251 (ttp)
REVERT: B  396 GLU cc_start: 0.8304 (tp30) cc_final: 0.8076 (tp30)
REVERT: B  992 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7171 (tm-30)
REVERT: B 1002 MET cc_start: 0.8571 (mtp) cc_final: 0.8371 (mtm)
REVERT: B 1016 GLU cc_start: 0.7544 (pt0) cc_final: 0.6872 (mt-10)
  outliers start: 16
  outliers final: 12
  residues processed: 113
  average time/residue: 1.1937
  time to fit residues: 142.7915
Evaluate side-chains
  112 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ASN
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  379 HIS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  418 ASP
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue  976 GLU
Chi-restraints excluded: chain A residue  990 ASP
Chi-restraints excluded: chain A residue 1060 MET
Chi-restraints excluded: chain A residue 1130 VAL
Chi-restraints excluded: chain B residue   94 GLN
Chi-restraints excluded: chain B residue  366 THR
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  992 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 54 optimal weight:    0.2980
   chunk 65 optimal weight:    0.4980
   chunk 52 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1158 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.148367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.121192 restraints weight = 7504.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.26
r_work: 0.3307 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7502  Z= 0.130
  Angle     :  0.572   8.734  10176  Z= 0.288
  Chirality :  0.043   0.161   1119
  Planarity :  0.004   0.036   1293
  Dihedral  : 10.827  99.990   1214
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.23 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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:  0.80 (0.30), residues: 841
  helix:  1.54 (0.28), residues: 373
  sheet: -0.18 (0.55), residues: 94
  loop : -0.24 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 416 
 HIS   0.011   0.001   HIS B 987 
 PHE   0.027   0.002   PHE A 982 
 TYR   0.015   0.001   TYR B 331 
 ARG   0.002   0.000   ARG A 986 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00190 (    7)
  link_NAG-ASN         : angle       1.70810 (   21)
  link_BETA1-4         : bond        0.00407 (    1)
  link_BETA1-4         : angle       1.01871 (    3)
  hydrogen bonds       : bond        0.03728 (  294)
  hydrogen bonds       : angle       4.33978 (  852)
  SS BOND              : bond        0.00129 (    1)
  SS BOND              : angle       0.20884 (    2)
  covalent geometry    : bond        0.00300 ( 7493)
  covalent geometry    : angle       0.56749 (10150)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9530.76 seconds
wall clock time: 165 minutes 41.58 seconds (9941.58 seconds total)