Starting phenix.real_space_refine
on Wed Sep 17 07:56:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c7u_45294/09_2025/9c7u_45294_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c7u_45294/09_2025/9c7u_45294.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c7u_45294/09_2025/9c7u_45294.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c7u_45294/09_2025/9c7u_45294.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c7u_45294/09_2025/9c7u_45294_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c7u_45294/09_2025/9c7u_45294_neut.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4356      2.51       5
     N    1189      2.21       5
     O    1276      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6848
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3979
          Classifications: {'peptide': 505}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 17, 'TRANS': 487}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 1482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1482
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 10, 'TRANS': 175}
    Chain: "C"
      Number of atoms: 1373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1373
          Classifications: {'peptide': 205}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 3, 'TRANS': 201}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 263
          Unresolved non-hydrogen angles: 338
          Unresolved non-hydrogen dihedrals: 226
          Unresolved non-hydrogen chiralities: 28
          Planarities with less than four sites: {'PHE:plan': 9, 'TRP:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 3, 'GLU:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 137
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.73, per 1000 atoms: 0.25
  Number of scatterers: 6848
  At special positions: 0
  Unit cell: (61.568, 79.872, 160.576, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1276      8.00
     N    1189      7.00
     C    4356      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 692 " - pdb=" SG  CYS B 716 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 428 "
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 375.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1692

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 7 sheets defined
      45.5% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 92
      No H-bonds generated for 'chain 'A' and resid 90 through 92'
    Processing helix  chain 'A' and resid 93 through 103
    Processing helix  chain 'A' and resid 120 through 136
      removed outlier: 3.637A  pdb=" N   GLU A 131 " --> pdb=" O   PHE A 127 " (cutoff:3.500A)
      Proline residue:  A 132  - end of helix
    Processing helix  chain 'A' and resid 149 through 165
      removed outlier: 3.591A  pdb=" N   ALA A 164 " --> pdb=" O   GLN A 160 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   SER A 165 " --> pdb=" O   ALA A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 180
    Processing helix  chain 'A' and resid 231 through 235
    Processing helix  chain 'A' and resid 241 through 261
      removed outlier: 3.809A  pdb=" N   SER A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   VAL A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   TYR A 261 " --> pdb=" O   ARG A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 265
    Processing helix  chain 'A' and resid 282 through 292
    Processing helix  chain 'A' and resid 332 through 348
    Processing helix  chain 'A' and resid 371 through 378
      removed outlier: 4.031A  pdb=" N   PHE A 375 " --> pdb=" O   GLU A 371 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ARG A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 406
    Processing helix  chain 'A' and resid 407 through 427
    Processing helix  chain 'A' and resid 429 through 433
      removed outlier: 4.044A  pdb=" N   GLY A 433 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 462
      removed outlier: 4.233A  pdb=" N   GLN A 462 " --> pdb=" O   TRP A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 485
    Processing helix  chain 'A' and resid 521 through 553
      removed outlier: 3.747A  pdb=" N   ASP A 525 " --> pdb=" O   PRO A 521 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL A 543 " --> pdb=" O   ALA A 539 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   GLN A 544 " --> pdb=" O   TYR A 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 689 through 695
      removed outlier: 4.138A  pdb=" N   ILE B 694 " --> pdb=" O   ASP B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 773 through 775
      No H-bonds generated for 'chain 'B' and resid 773 through 775'
    Processing helix  chain 'C' and resid 3 through 24
      removed outlier: 3.837A  pdb=" N   PHE C  15 " --> pdb=" O   ALA C  11 " (cutoff:3.500A)
      Proline residue:  C  16  - end of helix
    Processing helix  chain 'C' and resid 25 through 29
    Processing helix  chain 'C' and resid 31 through 56
    Processing helix  chain 'C' and resid 69 through 91
      removed outlier: 3.860A  pdb=" N   ASN C  91 " --> pdb=" O   VAL C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 3.760A  pdb=" N   GLY C 105 " --> pdb=" O   VAL C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 122
    Processing helix  chain 'C' and resid 130 through 157
      removed outlier: 3.522A  pdb=" N   LEU C 143 " --> pdb=" O   SER C 139 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   VAL C 144 " --> pdb=" O   ASN C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 177
    Processing helix  chain 'C' and resid 178 through 190
    Processing helix  chain 'C' and resid 194 through 220
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47
      removed outlier: 3.538A  pdb=" N   HIS A  44 " --> pdb=" O   ALA A 516 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR A  70 " --> pdb=" O   MET A 186 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50
      removed outlier: 6.229A  pdb=" N   VAL A 108 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   ALA A 146 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ILE A 110 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56
    Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 358
      removed outlier: 3.768A  pdb=" N   SER A 355 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A 322 " --> pdb=" O   SER A 355 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   VAL A 308 " --> pdb=" O   PHE A 383 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   LEU A 385 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   CYS A 310 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   LEU A 309 " --> pdb=" O   THR A 218 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   VAL A 220 " --> pdb=" O   LEU A 309 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   LEU A 311 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ILE A 219 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   PHE A 273 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ILE A 221 " --> pdb=" O   PHE A 273 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   SER A 275 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ILE A 201 " --> pdb=" O   HIS A 494 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   HIS A 494 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   SER A 203 " --> pdb=" O   GLN A 492 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   GLN A 492 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   GLU A 205 " --> pdb=" O   VAL A 490 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   VAL A 490 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 669 through 672
      removed outlier: 6.558A  pdb=" N   THR B 670 " --> pdb=" O   ILE B 752 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   VAL B 754 " --> pdb=" O   THR B 670 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   SER B 672 " --> pdb=" O   VAL B 754 " (cutoff:3.500A)
      removed outlier: 8.504A  pdb=" N   ARG B 756 " --> pdb=" O   SER B 672 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 698 through 700
      removed outlier: 3.919A  pdb=" N   GLU B 685 " --> pdb=" O   GLN B 721 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   TYR B 718 " --> pdb=" O   ILE B 740 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ILE B 740 " --> pdb=" O   TYR B 718 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL B 720 " --> pdb=" O   ARG B 738 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ARG B 738 " --> pdb=" O   VAL B 720 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 777 through 779

    311 hydrogen bonds defined for protein.
    888 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.07

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2282
        1.34 -     1.46: 1383
        1.46 -     1.58: 3276
        1.58 -     1.69: 0
        1.69 -     1.81: 47
  Bond restraints: 6988
  Sorted by residual:
  bond pdb=" C5  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.23e+00
  bond pdb=" N   ASP A 525 "
       pdb=" CA  ASP A 525 "
    ideal  model  delta    sigma   weight residual
    1.458  1.445  0.013 1.30e-02 5.92e+03 9.55e-01
  bond pdb=" C3  NAG A 601 "
       pdb=" O3  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.403  1.422 -0.019 2.00e-02 2.50e+03 9.36e-01
  bond pdb=" CA  GLU A 431 "
       pdb=" CB  GLU A 431 "
    ideal  model  delta    sigma   weight residual
    1.524  1.538 -0.014 1.51e-02 4.39e+03 8.76e-01
  bond pdb=" CB  ILE A 155 "
       pdb=" CG2 ILE A 155 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.37e-01
  ... (remaining 6983 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 9342
        1.93 -     3.86: 137
        3.86 -     5.80: 19
        5.80 -     7.73: 6
        7.73 -     9.66: 3
  Bond angle restraints: 9507
  Sorted by residual:
  angle pdb=" CA  GLU A 431 "
        pdb=" CB  GLU A 431 "
        pdb=" CG  GLU A 431 "
      ideal   model   delta    sigma   weight residual
     114.10  122.25   -8.15 2.00e+00 2.50e-01 1.66e+01
  angle pdb=" CB  MET A 456 "
        pdb=" CG  MET A 456 "
        pdb=" SD  MET A 456 "
      ideal   model   delta    sigma   weight residual
     112.70  122.36   -9.66 3.00e+00 1.11e-01 1.04e+01
  angle pdb=" CB  ARG A 339 "
        pdb=" CG  ARG A 339 "
        pdb=" CD  ARG A 339 "
      ideal   model   delta    sigma   weight residual
     111.30  117.24   -5.94 2.30e+00 1.89e-01 6.66e+00
  angle pdb=" N   PHE C   4 "
        pdb=" CA  PHE C   4 "
        pdb=" C   PHE C   4 "
      ideal   model   delta    sigma   weight residual
     112.54  109.44    3.10 1.22e+00 6.72e-01 6.44e+00
  angle pdb=" C   GLU A 431 "
        pdb=" CA  GLU A 431 "
        pdb=" CB  GLU A 431 "
      ideal   model   delta    sigma   weight residual
     111.40  114.64   -3.24 1.29e+00 6.01e-01 6.31e+00
  ... (remaining 9502 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 3563
       17.86 -    35.71: 457
       35.71 -    53.57: 114
       53.57 -    71.43: 22
       71.43 -    89.28: 5
  Dihedral angle restraints: 4161
    sinusoidal: 1545
      harmonic: 2616
  Sorted by residual:
  dihedral pdb=" CA  SER A 397 "
           pdb=" C   SER A 397 "
           pdb=" N   SER A 398 "
           pdb=" CA  SER A 398 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  ILE A 130 "
           pdb=" C   ILE A 130 "
           pdb=" N   GLU A 131 "
           pdb=" CA  GLU A 131 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.12  -18.88     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  THR A  74 "
           pdb=" C   THR A  74 "
           pdb=" N   MET A  75 "
           pdb=" CA  MET A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.41  -18.59     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 4158 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 862
       0.046 -    0.092: 180
       0.092 -    0.138: 53
       0.138 -    0.184: 0
       0.184 -    0.230: 1
  Chirality restraints: 1096
  Sorted by residual:
  chirality pdb=" C1  NAG A 601 "
            pdb=" ND2 ASN A 428 "
            pdb=" C2  NAG A 601 "
            pdb=" O5  NAG A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  THR A 313 "
            pdb=" N   THR A 313 "
            pdb=" C   THR A 313 "
            pdb=" CB  THR A 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.00e-01
  chirality pdb=" CA  VAL B 815 "
            pdb=" N   VAL B 815 "
            pdb=" C   VAL B 815 "
            pdb=" CB  VAL B 815 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 1093 not shown)

  Planarity restraints: 1228
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C   4 "   -0.018 2.00e-02 2.50e+03   1.86e-02 6.06e+00
        pdb=" CG  PHE C   4 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 PHE C   4 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE C   4 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE C   4 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE C   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C   4 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 434 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO A 435 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 435 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 435 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 778 "   -0.013 2.00e-02 2.50e+03   9.88e-03 2.44e+00
        pdb=" CG  TRP B 778 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 778 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 778 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 778 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 778 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 778 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 778 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 778 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 778 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1225 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 193
        2.69 -     3.24: 6982
        3.24 -     3.80: 10900
        3.80 -     4.35: 13433
        4.35 -     4.90: 22381
  Nonbonded interactions: 53889
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 258 "
            pdb=" OG1 THR A 264 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" OG  SER A 256 "
            pdb=" O   TYR A 486 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" N   GLU C 127 "
            pdb=" OE1 GLU C 127 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" OD1 ASP A 525 "
            pdb=" ND2 ASN C   8 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" OD1 ASN B 813 "
            pdb=" OG1 THR B 837 "
     model   vdw
     2.264 3.040
  ... (remaining 53884 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.100
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.290
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
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   0.036   6990  Z= 0.149
  Angle     :  0.614   9.660   9512  Z= 0.326
  Chirality :  0.041   0.230   1096
  Planarity :  0.004   0.043   1227
  Dihedral  : 16.991  89.285   2466
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 33.28 %
    Favored  : 66.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.30), residues: 882
  helix:  2.11 (0.27), residues: 367
  sheet: -2.40 (0.42), residues: 157
  loop : -2.42 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 464 
 TYR   0.020   0.001   TYR C 216 
 PHE   0.043   0.002   PHE C   4 
 TRP   0.027   0.002   TRP B 778 
 HIS   0.005   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6988)
  covalent geometry    : angle       0.61135 ( 9507)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       0.22643 (    2)
  hydrogen bonds       : bond        0.13090 (  311)
  hydrogen bonds       : angle       5.29115 (  888)
  link_NAG-ASN         : bond        0.00430 (    1)
  link_NAG-ASN         : angle       3.01834 (    3)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A  450 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7743 (pt0)
  outliers start: 2
  outliers final: 1
  residues processed: 108
  average time/residue: 0.0659
  time to fit residues: 10.2175
Evaluate side-chains
  102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain B residue  792 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0050
   chunk 51 optimal weight:    0.4980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 GLN
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.159118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.118185 restraints weight = 10278.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.121587 restraints weight = 5801.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.123684 restraints weight = 4087.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.125037 restraints weight = 3301.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.125732 restraints weight = 2904.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.0628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6990  Z= 0.147
  Angle     :  0.570   8.969   9512  Z= 0.296
  Chirality :  0.043   0.228   1096
  Planarity :  0.004   0.045   1227
  Dihedral  :  6.063  83.625    996
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 28.63 %
    Favored  : 66.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.30), residues: 882
  helix:  2.17 (0.27), residues: 362
  sheet: -2.34 (0.41), residues: 157
  loop : -2.30 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 413 
 TYR   0.011   0.001   TYR C  29 
 PHE   0.014   0.002   PHE A 441 
 TRP   0.016   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6988)
  covalent geometry    : angle       0.56712 ( 9507)
  SS BOND              : bond        0.00139 (    1)
  SS BOND              : angle       0.23538 (    2)
  hydrogen bonds       : bond        0.03188 (  311)
  hydrogen bonds       : angle       4.30411 (  888)
  link_NAG-ASN         : bond        0.00611 (    1)
  link_NAG-ASN         : angle       3.08774 (    3)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.7760 (ttp) cc_final: 0.7528 (ttp)
REVERT: B  809 ARG cc_start: 0.8505 (ptm-80) cc_final: 0.8149 (ptm-80)
  outliers start: 31
  outliers final: 21
  residues processed: 140
  average time/residue: 0.0696
  time to fit residues: 13.7303
Evaluate side-chains
  121 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  690 ASN
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  819 ASP
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 35 optimal weight:    0.1980
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0980
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A  44 HIS
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.160017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.119262 restraints weight = 10139.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.122703 restraints weight = 5706.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.124715 restraints weight = 4029.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.126177 restraints weight = 3270.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.126889 restraints weight = 2865.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.0979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6990  Z= 0.126
  Angle     :  0.560  11.165   9512  Z= 0.288
  Chirality :  0.042   0.219   1096
  Planarity :  0.004   0.041   1227
  Dihedral  :  4.856  43.500    990
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 29.22 %
    Favored  : 65.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.30), residues: 882
  helix:  2.19 (0.27), residues: 362
  sheet: -2.25 (0.41), residues: 165
  loop : -2.36 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 732 
 TYR   0.009   0.001   TYR A 261 
 PHE   0.011   0.001   PHE A 441 
 TRP   0.012   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6988)
  covalent geometry    : angle       0.55748 ( 9507)
  SS BOND              : bond        0.00178 (    1)
  SS BOND              : angle       0.34506 (    2)
  hydrogen bonds       : bond        0.03018 (  311)
  hydrogen bonds       : angle       4.12634 (  888)
  link_NAG-ASN         : bond        0.00567 (    1)
  link_NAG-ASN         : angle       3.05527 (    3)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 113
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: B  704 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8181 (pp20)
REVERT: B  809 ARG cc_start: 0.8489 (ptm-80) cc_final: 0.8129 (ptm-80)
  outliers start: 36
  outliers final: 26
  residues processed: 139
  average time/residue: 0.0725
  time to fit residues: 13.9778
Evaluate side-chains
  132 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  704 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    8.9990
   chunk 76 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.144375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.106451 restraints weight = 10649.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.106988 restraints weight = 6764.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.108958 restraints weight = 4839.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.109198 restraints weight = 3826.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.109511 restraints weight = 3627.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.1125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6990  Z= 0.166
  Angle     :  0.558   6.837   9512  Z= 0.292
  Chirality :  0.043   0.212   1096
  Planarity :  0.004   0.037   1227
  Dihedral  :  4.671  30.185    990
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 28.49 %
    Favored  : 64.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.30), residues: 882
  helix:  2.00 (0.27), residues: 368
  sheet: -2.22 (0.41), residues: 159
  loop : -2.32 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  82 
 TYR   0.010   0.001   TYR A 486 
 PHE   0.015   0.002   PHE C 128 
 TRP   0.011   0.001   TRP B 778 
 HIS   0.004   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6988)
  covalent geometry    : angle       0.55621 ( 9507)
  SS BOND              : bond        0.00178 (    1)
  SS BOND              : angle       0.34209 (    2)
  hydrogen bonds       : bond        0.03032 (  311)
  hydrogen bonds       : angle       4.08521 (  888)
  link_NAG-ASN         : bond        0.00387 (    1)
  link_NAG-ASN         : angle       2.87902 (    3)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 105
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.8046 (ttp) cc_final: 0.7732 (ttp)
REVERT: C   21 TYR cc_start: 0.6058 (OUTLIER) cc_final: 0.5266 (t80)
REVERT: C  113 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8089 (tpp)
  outliers start: 45
  outliers final: 32
  residues processed: 135
  average time/residue: 0.0688
  time to fit residues: 13.1374
Evaluate side-chains
  130 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 96
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain B residue  819 ASP
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  113 MET
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  211 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 27 optimal weight:    0.3980
   chunk 43 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0050
   chunk 42 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  59 GLN
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.144602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.105824 restraints weight = 10640.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.108271 restraints weight = 6264.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.109930 restraints weight = 4352.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.109918 restraints weight = 3418.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.110086 restraints weight = 3495.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6990  Z= 0.143
  Angle     :  0.555   8.449   9512  Z= 0.286
  Chirality :  0.042   0.205   1096
  Planarity :  0.004   0.037   1227
  Dihedral  :  4.530  20.853    990
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 29.22 %
    Favored  : 64.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.30), residues: 882
  helix:  2.05 (0.27), residues: 369
  sheet: -2.16 (0.42), residues: 157
  loop : -2.27 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  50 
 TYR   0.011   0.001   TYR C  97 
 PHE   0.014   0.002   PHE B 836 
 TRP   0.012   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6988)
  covalent geometry    : angle       0.55279 ( 9507)
  SS BOND              : bond        0.00174 (    1)
  SS BOND              : angle       0.35217 (    2)
  hydrogen bonds       : bond        0.02966 (  311)
  hydrogen bonds       : angle       4.04084 (  888)
  link_NAG-ASN         : bond        0.00407 (    1)
  link_NAG-ASN         : angle       2.69500 (    3)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 105
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.8043 (ttp) cc_final: 0.7721 (ttp)
REVERT: B  786 ASN cc_start: 0.7373 (OUTLIER) cc_final: 0.6730 (p0)
REVERT: C   21 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.5199 (t80)
REVERT: C  115 ARG cc_start: 0.7310 (mtt90) cc_final: 0.7080 (ttm-80)
  outliers start: 42
  outliers final: 30
  residues processed: 134
  average time/residue: 0.0732
  time to fit residues: 13.8125
Evaluate side-chains
  132 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 100
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  786 ASN
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 82 optimal weight:    9.9990
   chunk 79 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0670
   chunk 71 optimal weight:    8.9990
   chunk 8 optimal weight:    0.4980
   chunk 55 optimal weight:    4.9990
   chunk 70 optimal weight:    0.1980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A  44 HIS
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.145745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.104703 restraints weight = 10564.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.108038 restraints weight = 5893.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.110160 restraints weight = 4139.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.111353 restraints weight = 3333.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.112330 restraints weight = 2938.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6990  Z= 0.129
  Angle     :  0.549   7.380   9512  Z= 0.283
  Chirality :  0.042   0.199   1096
  Planarity :  0.004   0.036   1227
  Dihedral  :  4.397  20.749    990
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  6.54 %
    Allowed  : 29.65 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.30), residues: 882
  helix:  2.17 (0.27), residues: 368
  sheet: -2.18 (0.42), residues: 157
  loop : -2.26 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 339 
 TYR   0.011   0.001   TYR A 486 
 PHE   0.014   0.002   PHE C 128 
 TRP   0.012   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6988)
  covalent geometry    : angle       0.54730 ( 9507)
  SS BOND              : bond        0.00175 (    1)
  SS BOND              : angle       0.34689 (    2)
  hydrogen bonds       : bond        0.02902 (  311)
  hydrogen bonds       : angle       3.93635 (  888)
  link_NAG-ASN         : bond        0.00413 (    1)
  link_NAG-ASN         : angle       2.50338 (    3)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 109
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.8053 (ttp) cc_final: 0.7730 (ttp)
REVERT: B  786 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.6683 (p0)
REVERT: C   21 TYR cc_start: 0.6104 (OUTLIER) cc_final: 0.5232 (t80)
  outliers start: 45
  outliers final: 33
  residues processed: 140
  average time/residue: 0.0678
  time to fit residues: 13.4014
Evaluate side-chains
  137 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 102
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  786 ASN
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  211 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0170
   chunk 80 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.144509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.103763 restraints weight = 10536.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.107065 restraints weight = 5954.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.109035 restraints weight = 4196.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.110481 restraints weight = 3410.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.111205 restraints weight = 2979.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6990  Z= 0.157
  Angle     :  0.578   8.826   9512  Z= 0.295
  Chirality :  0.043   0.253   1096
  Planarity :  0.004   0.036   1227
  Dihedral  :  4.396  20.878    990
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  7.27 %
    Allowed  : 29.07 %
    Favored  : 63.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.30), residues: 882
  helix:  2.14 (0.27), residues: 369
  sheet: -2.23 (0.42), residues: 157
  loop : -2.25 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.013   0.001   TYR A 486 
 PHE   0.012   0.002   PHE C  18 
 TRP   0.012   0.001   TRP B 778 
 HIS   0.004   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6988)
  covalent geometry    : angle       0.57580 ( 9507)
  SS BOND              : bond        0.00177 (    1)
  SS BOND              : angle       0.35343 (    2)
  hydrogen bonds       : bond        0.02936 (  311)
  hydrogen bonds       : angle       3.97016 (  888)
  link_NAG-ASN         : bond        0.00597 (    1)
  link_NAG-ASN         : angle       2.74143 (    3)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 104
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  356 MET cc_start: 0.8139 (ttp) cc_final: 0.7859 (ttp)
REVERT: B  786 ASN cc_start: 0.7360 (OUTLIER) cc_final: 0.6699 (p0)
REVERT: B  809 ARG cc_start: 0.8460 (ptm-80) cc_final: 0.8247 (ptm-80)
REVERT: C   21 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5263 (t80)
REVERT: C  143 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8370 (tt)
  outliers start: 50
  outliers final: 36
  residues processed: 140
  average time/residue: 0.0658
  time to fit residues: 13.1240
Evaluate side-chains
  141 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 102
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  786 ASN
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  808 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Chi-restraints excluded: chain C residue  211 SER
Chi-restraints excluded: chain C residue  215 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 7 optimal weight:    0.2980
   chunk 42 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.144589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.104079 restraints weight = 10631.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.107348 restraints weight = 5943.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.109432 restraints weight = 4165.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.110507 restraints weight = 3362.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.111460 restraints weight = 2977.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6990  Z= 0.146
  Angle     :  0.589  11.089   9512  Z= 0.297
  Chirality :  0.043   0.258   1096
  Planarity :  0.004   0.035   1227
  Dihedral  :  4.393  20.819    990
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.41 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 30.52 %
    Favored  : 63.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.30), residues: 882
  helix:  2.15 (0.27), residues: 368
  sheet: -2.20 (0.41), residues: 157
  loop : -2.26 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.016   0.001   TYR A 261 
 PHE   0.012   0.002   PHE C  18 
 TRP   0.014   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6988)
  covalent geometry    : angle       0.58711 ( 9507)
  SS BOND              : bond        0.00177 (    1)
  SS BOND              : angle       0.35199 (    2)
  hydrogen bonds       : bond        0.02923 (  311)
  hydrogen bonds       : angle       3.94900 (  888)
  link_NAG-ASN         : bond        0.00524 (    1)
  link_NAG-ASN         : angle       2.76389 (    3)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 104
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  356 MET cc_start: 0.8123 (ttp) cc_final: 0.7833 (ttp)
REVERT: B  749 ASP cc_start: 0.9057 (t0) cc_final: 0.8762 (t0)
REVERT: B  786 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.6934 (p0)
REVERT: B  809 ARG cc_start: 0.8431 (ptm-80) cc_final: 0.8214 (ptm-80)
REVERT: C   21 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.5366 (t80)
REVERT: C  201 ARG cc_start: 0.8712 (mtm-85) cc_final: 0.8139 (mtm110)
  outliers start: 43
  outliers final: 33
  residues processed: 137
  average time/residue: 0.0691
  time to fit residues: 13.3583
Evaluate side-chains
  135 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 100
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  139 THR
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  786 ASN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 38 optimal weight:    0.0030
   chunk 26 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   chunk 29 optimal weight:    0.6980
   chunk 51 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0060
   chunk 81 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.4806

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.145553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.104907 restraints weight = 10612.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.108177 restraints weight = 5953.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.110295 restraints weight = 4193.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.111497 restraints weight = 3398.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.112324 restraints weight = 2982.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6990  Z= 0.131
  Angle     :  0.601  14.277   9512  Z= 0.298
  Chirality :  0.043   0.284   1096
  Planarity :  0.004   0.035   1227
  Dihedral  :  4.343  20.845    990
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 31.40 %
    Favored  : 63.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.30), residues: 882
  helix:  2.18 (0.27), residues: 368
  sheet: -2.11 (0.42), residues: 157
  loop : -2.23 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.013   0.001   TYR A 486 
 PHE   0.013   0.001   PHE C  18 
 TRP   0.012   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6988)
  covalent geometry    : angle       0.59920 ( 9507)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.33684 (    2)
  hydrogen bonds       : bond        0.02890 (  311)
  hydrogen bonds       : angle       3.91226 (  888)
  link_NAG-ASN         : bond        0.00515 (    1)
  link_NAG-ASN         : angle       2.79737 (    3)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  356 MET cc_start: 0.8075 (ttp) cc_final: 0.7795 (ttp)
REVERT: B  749 ASP cc_start: 0.9046 (t0) cc_final: 0.8755 (t0)
REVERT: B  786 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.6875 (p0)
REVERT: B  809 ARG cc_start: 0.8423 (ptm-80) cc_final: 0.8205 (ptm-80)
REVERT: B  812 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6992 (mm-30)
REVERT: C   21 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5362 (t80)
REVERT: C  115 ARG cc_start: 0.7066 (ttm-80) cc_final: 0.6439 (ttm-80)
REVERT: C  201 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8128 (mtm110)
  outliers start: 36
  outliers final: 31
  residues processed: 131
  average time/residue: 0.0682
  time to fit residues: 12.8089
Evaluate side-chains
  135 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 101
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  751 ASN
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  786 ASN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 57 optimal weight:    9.9990
   chunk 47 optimal weight:    0.0970
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    0.1980
   chunk 11 optimal weight:    0.6980
   chunk 82 optimal weight:    0.4980
   chunk 58 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.146498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.105547 restraints weight = 10568.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.108828 restraints weight = 5946.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.110986 restraints weight = 4205.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.112167 restraints weight = 3401.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.113007 restraints weight = 3000.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
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      :  0.003   0.039   6990  Z= 0.125
  Angle     :  0.605  13.979   9512  Z= 0.299
  Chirality :  0.043   0.315   1096
  Planarity :  0.004   0.035   1227
  Dihedral  :  4.290  20.825    990
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 31.54 %
    Favored  : 63.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.30), residues: 882
  helix:  2.20 (0.27), residues: 368
  sheet: -2.09 (0.42), residues: 157
  loop : -2.21 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.014   0.001   TYR A 486 
 PHE   0.015   0.001   PHE C   4 
 TRP   0.012   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6988)
  covalent geometry    : angle       0.60283 ( 9507)
  SS BOND              : bond        0.00171 (    1)
  SS BOND              : angle       0.34872 (    2)
  hydrogen bonds       : bond        0.02849 (  311)
  hydrogen bonds       : angle       3.85875 (  888)
  link_NAG-ASN         : bond        0.00536 (    1)
  link_NAG-ASN         : angle       2.82412 (    3)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 103
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  356 MET cc_start: 0.8034 (ttp) cc_final: 0.7754 (ttp)
REVERT: B  749 ASP cc_start: 0.9041 (t0) cc_final: 0.8726 (t0)
REVERT: B  786 ASN cc_start: 0.7222 (OUTLIER) cc_final: 0.6792 (p0)
REVERT: B  809 ARG cc_start: 0.8430 (ptm-80) cc_final: 0.8206 (ptm-80)
REVERT: B  812 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7008 (mm-30)
REVERT: C   21 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.5427 (t80)
REVERT: C  115 ARG cc_start: 0.7174 (ttm-80) cc_final: 0.6731 (ttm-80)
REVERT: C  201 ARG cc_start: 0.8697 (mtm-85) cc_final: 0.8118 (mtm110)
  outliers start: 35
  outliers final: 29
  residues processed: 129
  average time/residue: 0.0663
  time to fit residues: 12.3238
Evaluate side-chains
  135 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 103
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  243 SER
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  397 SER
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  763 LEU
Chi-restraints excluded: chain B residue  786 ASN
Chi-restraints excluded: chain B residue  807 LEU
Chi-restraints excluded: chain B residue  812 GLU
Chi-restraints excluded: chain B residue  813 ASN
Chi-restraints excluded: chain C residue   21 TYR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  126 ILE
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  208 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 18 optimal weight:    0.1980
   chunk 75 optimal weight:    8.9990
   chunk 41 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 78 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 71 optimal weight:    8.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.145510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.104943 restraints weight = 10532.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.108230 restraints weight = 5947.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.110119 restraints weight = 4192.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.111593 restraints weight = 3413.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.112379 restraints weight = 2983.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6990  Z= 0.137
  Angle     :  0.592  11.122   9512  Z= 0.298
  Chirality :  0.043   0.309   1096
  Planarity :  0.004   0.035   1227
  Dihedral  :  4.283  20.938    990
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 31.25 %
    Favored  : 63.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.30), residues: 882
  helix:  2.21 (0.27), residues: 368
  sheet: -2.09 (0.42), residues: 157
  loop : -2.20 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 339 
 TYR   0.014   0.001   TYR A 486 
 PHE   0.022   0.002   PHE C   4 
 TRP   0.012   0.001   TRP B 778 
 HIS   0.005   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6988)
  covalent geometry    : angle       0.58964 ( 9507)
  SS BOND              : bond        0.00170 (    1)
  SS BOND              : angle       0.34772 (    2)
  hydrogen bonds       : bond        0.02856 (  311)
  hydrogen bonds       : angle       3.85578 (  888)
  link_NAG-ASN         : bond        0.00530 (    1)
  link_NAG-ASN         : angle       2.81750 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1439.14 seconds
wall clock time: 25 minutes 39.97 seconds (1539.97 seconds total)