Starting phenix.real_space_refine
on Sun May 11 15:13:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8irm_35679/05_2025/8irm_35679.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8irm_35679/05_2025/8irm_35679.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8irm_35679/05_2025/8irm_35679.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8irm_35679/05_2025/8irm_35679.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8irm_35679/05_2025/8irm_35679.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8irm_35679/05_2025/8irm_35679.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5290      2.51       5
     N    1316      2.21       5
     O    1472      1.98       5
     H       8      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8138
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4026
          Classifications: {'peptide': 540}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516}
    Chain: "B"
      Number of atoms: 4026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4026
          Classifications: {'peptide': 540}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'ADE': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'ADE': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 5.55, per 1000 atoms: 0.68
  Number of scatterers: 8138
  At special positions: 0
  Unit cell: (93.61, 104.673, 100.418, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     O    1472      8.00
     N    1316      7.00
     C    5290      6.00
     H       8      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  78 " - pdb=" SG  CYS A 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  83 " - pdb=" SG  CYS A 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  87 " - pdb=" SG  CYS A  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 254 " - pdb=" SG  CYS A 287 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  78 " - pdb=" SG  CYS B 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  83 " - pdb=" SG  CYS B 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  87 " - pdb=" SG  CYS B  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 254 " - pdb=" SG  CYS B 287 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 270 "
      " NAG D   1 " - " ASN B 270 "
  Time building additional restraints: 2.63
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1940

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 8 sheets defined
      68.1% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 31
    Processing helix  chain 'A' and resid 31 through 37
    Processing helix  chain 'A' and resid 39 through 43
    Processing helix  chain 'A' and resid 46 through 61
    Processing helix  chain 'A' and resid 62 through 74
      removed outlier: 4.389A  pdb=" N   ALA A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 93 through 97
    Processing helix  chain 'A' and resid 108 through 113
    Processing helix  chain 'A' and resid 117 through 149
    Processing helix  chain 'A' and resid 159 through 169
    Processing helix  chain 'A' and resid 180 through 202
      removed outlier: 3.500A  pdb=" N   ILE A 201 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 211
      removed outlier: 3.969A  pdb=" N   VAL A 211 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 232
      removed outlier: 4.255A  pdb=" N   SER A 220 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ALA A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 257
      No H-bonds generated for 'chain 'A' and resid 255 through 257'
    Processing helix  chain 'A' and resid 294 through 313
    Processing helix  chain 'A' and resid 317 through 331
    Processing helix  chain 'A' and resid 343 through 355
      removed outlier: 3.954A  pdb=" N   LYS A 355 " --> pdb=" O   ASP A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 374
      removed outlier: 4.562A  pdb=" N   GLY A 373 " --> pdb=" O   SER A 370 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ILE A 374 " --> pdb=" O   PHE A 371 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 370 through 374'
    Processing helix  chain 'A' and resid 376 through 405
      removed outlier: 3.586A  pdb=" N   TRP A 380 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   TYR A 399 " --> pdb=" O   THR A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 435
    Processing helix  chain 'A' and resid 444 through 452
      removed outlier: 4.039A  pdb=" N   GLY A 448 " --> pdb=" O   GLU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 470
    Processing helix  chain 'A' and resid 472 through 477
    Processing helix  chain 'A' and resid 480 through 496
      Proline residue:  A 486  - end of helix
      removed outlier: 3.566A  pdb=" N   ILE A 489 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 502
      removed outlier: 3.694A  pdb=" N   THR A 500 " --> pdb=" O   LYS A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 523
      Proline residue:  A 512  - end of helix
      Proline residue:  A 521  - end of helix
    Processing helix  chain 'A' and resid 525 through 554
      removed outlier: 4.581A  pdb=" N   TRP A 543 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   ASP A 544 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 30
    Processing helix  chain 'B' and resid 31 through 37
    Processing helix  chain 'B' and resid 46 through 61
    Processing helix  chain 'B' and resid 62 through 74
      removed outlier: 4.703A  pdb=" N   ALA B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER B  74 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
    Processing helix  chain 'B' and resid 93 through 97
    Processing helix  chain 'B' and resid 108 through 113
    Processing helix  chain 'B' and resid 117 through 149
      removed outlier: 3.519A  pdb=" N   VAL B 124 " --> pdb=" O   TYR B 120 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLU B 125 " --> pdb=" O   ALA B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 169
      removed outlier: 4.142A  pdb=" N   ALA B 164 " --> pdb=" O   MET B 160 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   TYR B 165 " --> pdb=" O   GLY B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 201
    Processing helix  chain 'B' and resid 203 through 209
    Processing helix  chain 'B' and resid 212 through 232
      removed outlier: 4.145A  pdb=" N   SER B 220 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA B 221 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 257
      No H-bonds generated for 'chain 'B' and resid 255 through 257'
    Processing helix  chain 'B' and resid 294 through 313
    Processing helix  chain 'B' and resid 317 through 331
    Processing helix  chain 'B' and resid 343 through 355
      removed outlier: 3.884A  pdb=" N   LYS B 355 " --> pdb=" O   ASP B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 405
      removed outlier: 3.735A  pdb=" N   TRP B 380 " --> pdb=" O   LYS B 376 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   PHE B 404 " --> pdb=" O   SER B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 435
      removed outlier: 3.537A  pdb=" N   MET B 422 " --> pdb=" O   TYR B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 452
      removed outlier: 4.232A  pdb=" N   GLY B 448 " --> pdb=" O   GLU B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 470
    Processing helix  chain 'B' and resid 472 through 477
    Processing helix  chain 'B' and resid 480 through 496
      Proline residue:  B 486  - end of helix
    Processing helix  chain 'B' and resid 497 through 502
      removed outlier: 3.559A  pdb=" N   THR B 500 " --> pdb=" O   LYS B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 523
      Proline residue:  B 512  - end of helix
      removed outlier: 3.769A  pdb=" N   MET B 520 " --> pdb=" O   THR B 516 " (cutoff:3.500A)
      Proline residue:  B 521  - end of helix
    Processing helix  chain 'B' and resid 525 through 541
    Processing helix  chain 'B' and resid 541 through 554
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158
    Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 244
    Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 275
      removed outlier: 3.810A  pdb=" N   SER A 261 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   SER B 261 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 287
      removed outlier: 3.810A  pdb=" N   SER A 261 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   SER B 261 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 87
    Processing sheet with id=AA7, first strand: chain 'B' and resid 156 through 158
    Processing sheet with id=AA8, first strand: chain 'B' and resid 241 through 242

    517 hydrogen bonds defined for protein.
    1467 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.73

  Time building geometry restraints manager: 2.93 seconds

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

  Histogram of bond lengths:
        0.86 -     1.05: 8
        1.05 -     1.24: 1111
        1.24 -     1.43: 2341
        1.43 -     1.62: 4780
        1.62 -     1.81: 84
  Bond restraints: 8324
  Sorted by residual:
  bond pdb=" C5  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.538 -0.125 2.00e-02 2.50e+03 3.93e+01
  bond pdb=" C5  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.535 -0.122 2.00e-02 2.50e+03 3.75e+01
  bond pdb=" C6  ADE A 701 "
       pdb=" N6  ADE A 701 "
    ideal  model  delta    sigma   weight residual
    1.334  1.449 -0.115 2.00e-02 2.50e+03 3.30e+01
  bond pdb=" C5  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.527 -0.114 2.00e-02 2.50e+03 3.26e+01
  bond pdb=" C6  ADE B 701 "
       pdb=" N6  ADE B 701 "
    ideal  model  delta    sigma   weight residual
    1.334  1.448 -0.114 2.00e-02 2.50e+03 3.26e+01
  ... (remaining 8319 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 11135
        2.26 -     4.51: 157
        4.51 -     6.77: 30
        6.77 -     9.03: 10
        9.03 -    11.29: 2
  Bond angle restraints: 11334
  Sorted by residual:
  angle pdb=" C   THR B  45 "
        pdb=" N   PHE B  46 "
        pdb=" CA  PHE B  46 "
      ideal   model   delta    sigma   weight residual
     122.15  110.86   11.29 2.83e+00 1.25e-01 1.59e+01
  angle pdb=" C   THR A  45 "
        pdb=" N   PHE A  46 "
        pdb=" CA  PHE A  46 "
      ideal   model   delta    sigma   weight residual
     122.15  111.15   11.00 2.83e+00 1.25e-01 1.51e+01
  angle pdb=" C   THR A 247 "
        pdb=" N   LEU A 248 "
        pdb=" CA  LEU A 248 "
      ideal   model   delta    sigma   weight residual
     121.54  127.59   -6.05 1.91e+00 2.74e-01 1.00e+01
  angle pdb=" N   TYR B 524 "
        pdb=" CA  TYR B 524 "
        pdb=" C   TYR B 524 "
      ideal   model   delta    sigma   weight residual
     112.58  108.84    3.74 1.22e+00 6.72e-01 9.42e+00
  angle pdb=" C2  ADE A 701 "
        pdb=" N3  ADE A 701 "
        pdb=" C4  ADE A 701 "
      ideal   model   delta    sigma   weight residual
     111.66  120.61   -8.95 3.00e+00 1.11e-01 8.90e+00
  ... (remaining 11329 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.48: 4650
       22.48 -    44.96: 213
       44.96 -    67.44: 27
       67.44 -    89.93: 3
       89.93 -   112.41: 3
  Dihedral angle restraints: 4896
    sinusoidal: 1844
      harmonic: 3052
  Sorted by residual:
  dihedral pdb=" CA  VAL B 484 "
           pdb=" C   VAL B 484 "
           pdb=" N   GLY B 485 "
           pdb=" CA  GLY B 485 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.58   37.42     0      5.00e+00 4.00e-02 5.60e+01
  dihedral pdb=" CA  VAL A 484 "
           pdb=" C   VAL A 484 "
           pdb=" N   GLY A 485 "
           pdb=" CA  GLY A 485 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.52   36.48     0      5.00e+00 4.00e-02 5.32e+01
  dihedral pdb=" CA  PHE B 332 "
           pdb=" C   PHE B 332 "
           pdb=" N   ARG B 333 "
           pdb=" CA  ARG B 333 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.26  -20.74     0      5.00e+00 4.00e-02 1.72e+01
  ... (remaining 4893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1081
       0.051 -    0.102: 242
       0.102 -    0.154: 27
       0.154 -    0.205: 3
       0.205 -    0.256: 3
  Chirality restraints: 1356
  Sorted by residual:
  chirality pdb=" C5  NAG C   1 "
            pdb=" C4  NAG C   1 "
            pdb=" C6  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.67    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CB  THR B 250 "
            pdb=" CA  THR B 250 "
            pdb=" OG1 THR B 250 "
            pdb=" CG2 THR B 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" C5  NAG C   2 "
            pdb=" C4  NAG C   2 "
            pdb=" C6  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.63    0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 1353 not shown)

  Planarity restraints: 1402
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 248 "    0.017 2.00e-02 2.50e+03   3.40e-02 1.16e+01
        pdb=" C   LEU A 248 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   LEU A 248 "    0.022 2.00e-02 2.50e+03
        pdb=" N   VAL A 249 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 486 "   -0.046 5.00e-02 4.00e+02   6.93e-02 7.68e+00
        pdb=" N   PRO A 487 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A 487 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 487 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 486 "   -0.041 5.00e-02 4.00e+02   6.16e-02 6.08e+00
        pdb=" N   PRO B 487 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B 487 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 487 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1399 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.60: 73
        2.60 -     3.10: 6265
        3.10 -     3.60: 10557
        3.60 -     4.10: 14423
        4.10 -     4.60: 23235
  Nonbonded interactions: 54553
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 539 "
            pdb=" OH  TYR B 309 "
     model   vdw
     2.101 2.800
  nonbonded pdb=" OD1 ASN A 163 "
            pdb=" OG  SER A 437 "
     model   vdw
     2.119 2.800
  nonbonded pdb=" OD1 ASN B  67 "
            pdb=" ND2 ASN B 163 "
     model   vdw
     2.126 2.950
  nonbonded pdb=" OG  SER A 268 "
            pdb=" OD1 ASN A 270 "
     model   vdw
     2.157 2.800
  nonbonded pdb=" OH  TYR A 309 "
            pdb=" O   VAL B 539 "
     model   vdw
     2.169 2.800
  ... (remaining 54548 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.800
  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:             0.230
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.120
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
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      :  0.007   0.125   8328  Z= 0.334
  Angle     :  0.690  11.285  11348  Z= 0.337
  Chirality :  0.042   0.256   1356
  Planarity :  0.005   0.069   1398
  Dihedral  : 13.129 112.406   2932
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.26), residues: 1076
  helix:  1.25 (0.20), residues: 660
  sheet: -4.69 (0.63), residues: 20
  loop : -0.18 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 331 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.035   0.002   PHE A 442 
 TYR   0.030   0.001   TYR A 418 
 ARG   0.001   0.000   ARG A  42 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00495 (    2)
  link_NAG-ASN         : angle       2.61063 (    6)
  link_BETA1-4         : bond        0.00805 (    2)
  link_BETA1-4         : angle       2.88367 (    6)
  hydrogen bonds       : bond        0.16928 (  513)
  hydrogen bonds       : angle       6.28256 ( 1467)
  SS BOND              : bond        0.00123 (    8)
  SS BOND              : angle       1.50960 (   16)
  covalent geometry    : bond        0.00690 ( 8316)
  covalent geometry    : angle       0.68272 (11320)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.6316 (mpp-170) cc_final: 0.5980 (mtm-85)
REVERT: B   32 ARG cc_start: 0.6378 (mpp-170) cc_final: 0.6040 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 1.2498
  time to fit residues: 131.3695
Evaluate side-chains
  83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0020
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 43 optimal weight:    6.9990
   chunk 84 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 98 optimal weight:    0.7980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 163 ASN ** 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 = 0.3390 r_free = 0.3390 target = 0.116172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.091411 restraints weight = 10542.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.81
r_work: 0.2955 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8328  Z= 0.103
  Angle     :  0.473   8.474  11348  Z= 0.246
  Chirality :  0.037   0.154   1356
  Planarity :  0.004   0.066   1398
  Dihedral  :  7.628 102.773   1230
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  6.76 %
    Favored  : 92.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.26), residues: 1076
  helix:  2.03 (0.20), residues: 664
  sheet: -4.70 (0.63), residues: 20
  loop : -0.15 (0.33), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 482 
 HIS   0.003   0.001   HIS B 378 
 PHE   0.016   0.001   PHE A 442 
 TYR   0.009   0.001   TYR A 418 
 ARG   0.003   0.000   ARG A  42 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00415 (    2)
  link_NAG-ASN         : angle       2.79477 (    6)
  link_BETA1-4         : bond        0.00688 (    2)
  link_BETA1-4         : angle       2.91028 (    6)
  hydrogen bonds       : bond        0.03834 (  513)
  hydrogen bonds       : angle       4.58513 ( 1467)
  SS BOND              : bond        0.00098 (    8)
  SS BOND              : angle       1.15265 (   16)
  covalent geometry    : bond        0.00202 ( 8316)
  covalent geometry    : angle       0.46218 (11320)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.859 
Fit side-chains
REVERT: B  548 GLU cc_start: 0.7397 (tp30) cc_final: 0.6692 (mt-10)
  outliers start: 9
  outliers final: 6
  residues processed: 92
  average time/residue: 1.2341
  time to fit residues: 120.9097
Evaluate side-chains
  89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  413 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 88 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   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  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  67 ASN ** 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 = 0.3388 r_free = 0.3388 target = 0.115820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.090809 restraints weight = 10595.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 1.84
r_work: 0.2927 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8328  Z= 0.103
  Angle     :  0.445   8.374  11348  Z= 0.228
  Chirality :  0.037   0.135   1356
  Planarity :  0.004   0.065   1398
  Dihedral  :  7.078 100.338   1230
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 18.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  7.46 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.27), residues: 1076
  helix:  2.44 (0.20), residues: 666
  sheet: -4.68 (0.65), residues: 20
  loop : -0.04 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 380 
 HIS   0.002   0.001   HIS B 364 
 PHE   0.018   0.001   PHE A 442 
 TYR   0.008   0.001   TYR B 399 
 ARG   0.002   0.000   ARG A 103 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00322 (    2)
  link_NAG-ASN         : angle       2.21539 (    6)
  link_BETA1-4         : bond        0.00584 (    2)
  link_BETA1-4         : angle       2.71990 (    6)
  hydrogen bonds       : bond        0.03567 (  513)
  hydrogen bonds       : angle       4.17085 ( 1467)
  SS BOND              : bond        0.00124 (    8)
  SS BOND              : angle       1.16328 (   16)
  covalent geometry    : bond        0.00218 ( 8316)
  covalent geometry    : angle       0.43587 (11320)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.818 
Fit side-chains
REVERT: B  401 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7141 (mtp)
REVERT: B  548 GLU cc_start: 0.7461 (tp30) cc_final: 0.6791 (mt-10)
  outliers start: 17
  outliers final: 6
  residues processed: 91
  average time/residue: 1.2217
  time to fit residues: 118.5718
Evaluate side-chains
  88 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  413 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  67 ASN ** 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 = 0.3346 r_free = 0.3346 target = 0.112786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.087213 restraints weight = 10492.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 1.86
r_work: 0.2902 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8328  Z= 0.140
  Angle     :  0.469   9.097  11348  Z= 0.240
  Chirality :  0.038   0.134   1356
  Planarity :  0.004   0.065   1398
  Dihedral  :  6.809  97.866   1230
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 18.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  8.51 %
    Favored  : 89.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.27), residues: 1076
  helix:  2.43 (0.20), residues: 666
  sheet: -4.82 (0.60), residues: 20
  loop : -0.15 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 380 
 HIS   0.003   0.001   HIS B 364 
 PHE   0.020   0.001   PHE A 442 
 TYR   0.009   0.001   TYR B 399 
 ARG   0.002   0.000   ARG B  42 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00287 (    2)
  link_NAG-ASN         : angle       2.30572 (    6)
  link_BETA1-4         : bond        0.00506 (    2)
  link_BETA1-4         : angle       2.74365 (    6)
  hydrogen bonds       : bond        0.03637 (  513)
  hydrogen bonds       : angle       4.18589 ( 1467)
  SS BOND              : bond        0.00091 (    8)
  SS BOND              : angle       0.93327 (   16)
  covalent geometry    : bond        0.00313 ( 8316)
  covalent geometry    : angle       0.46141 (11320)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
REVERT: A  470 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6833 (mtp)
REVERT: A  494 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8450 (mtp)
REVERT: B  548 GLU cc_start: 0.7399 (tp30) cc_final: 0.6615 (mt-10)
  outliers start: 18
  outliers final: 9
  residues processed: 84
  average time/residue: 1.2516
  time to fit residues: 111.9755
Evaluate side-chains
  90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  388 TYR
Chi-restraints excluded: chain A residue  470 MET
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  123 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  413 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 97 optimal weight:    6.9990
   chunk 42 optimal weight:    0.2980
   chunk 101 optimal weight:    0.9990
   chunk 104 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 163 ASN ** 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 = 0.3373 r_free = 0.3373 target = 0.114929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.090072 restraints weight = 10510.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 1.81
r_work: 0.2927 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8328  Z= 0.096
  Angle     :  0.431   9.422  11348  Z= 0.219
  Chirality :  0.037   0.131   1356
  Planarity :  0.004   0.065   1398
  Dihedral  :  6.430  94.664   1230
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 19.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  9.21 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.27), residues: 1076
  helix:  2.62 (0.20), residues: 666
  sheet: -4.88 (0.61), residues: 20
  loop : -0.09 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 380 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.010   0.001   PHE A 442 
 TYR   0.007   0.001   TYR B 399 
 ARG   0.001   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00269 (    2)
  link_NAG-ASN         : angle       2.10710 (    6)
  link_BETA1-4         : bond        0.00587 (    2)
  link_BETA1-4         : angle       2.88103 (    6)
  hydrogen bonds       : bond        0.03219 (  513)
  hydrogen bonds       : angle       4.04787 ( 1467)
  SS BOND              : bond        0.00071 (    8)
  SS BOND              : angle       1.12109 (   16)
  covalent geometry    : bond        0.00204 ( 8316)
  covalent geometry    : angle       0.42103 (11320)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
REVERT: A  401 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7389 (mpp)
REVERT: A  470 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6793 (mtp)
REVERT: A  494 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8426 (mtp)
REVERT: B  103 ARG cc_start: 0.7419 (ptt-90) cc_final: 0.7155 (ptt-90)
REVERT: B  401 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.6959 (mpp)
REVERT: B  548 GLU cc_start: 0.7371 (tp30) cc_final: 0.6565 (mt-10)
  outliers start: 15
  outliers final: 8
  residues processed: 90
  average time/residue: 1.1730
  time to fit residues: 112.7900
Evaluate side-chains
  93 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  470 MET
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  123 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  413 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 92 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 103 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0060
   overall best weight:    1.2004

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 163 ASN ** 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 = 0.3347 r_free = 0.3347 target = 0.112881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.087281 restraints weight = 10475.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 1.84
r_work: 0.2901 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8328  Z= 0.132
  Angle     :  0.460   9.958  11348  Z= 0.234
  Chirality :  0.038   0.124   1356
  Planarity :  0.004   0.065   1398
  Dihedral  :  6.215  90.093   1230
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 18.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  9.56 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.27), residues: 1076
  helix:  2.59 (0.20), residues: 666
  sheet: -4.82 (0.60), residues: 20
  loop : -0.14 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 380 
 HIS   0.002   0.001   HIS B 364 
 PHE   0.012   0.001   PHE A 442 
 TYR   0.008   0.001   TYR B 399 
 ARG   0.001   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00285 (    2)
  link_NAG-ASN         : angle       2.20247 (    6)
  link_BETA1-4         : bond        0.00535 (    2)
  link_BETA1-4         : angle       3.03055 (    6)
  hydrogen bonds       : bond        0.03497 (  513)
  hydrogen bonds       : angle       4.08485 ( 1467)
  SS BOND              : bond        0.00076 (    8)
  SS BOND              : angle       1.16253 (   16)
  covalent geometry    : bond        0.00295 ( 8316)
  covalent geometry    : angle       0.45022 (11320)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7503 (ptt-90) cc_final: 0.7204 (ptt-90)
REVERT: A  401 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7216 (mpp)
REVERT: A  470 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6833 (mtp)
REVERT: A  494 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8452 (mtp)
REVERT: B  103 ARG cc_start: 0.7454 (ptt-90) cc_final: 0.7162 (ptt-90)
REVERT: B  401 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.6829 (mpp)
REVERT: B  548 GLU cc_start: 0.7390 (tp30) cc_final: 0.6585 (mt-10)
  outliers start: 17
  outliers final: 9
  residues processed: 86
  average time/residue: 1.2714
  time to fit residues: 116.4599
Evaluate side-chains
  92 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  470 MET
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  123 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  413 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0970
   chunk 40 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0040
   chunk 87 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
A 541 HIS
** B 163 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 = 0.3381 r_free = 0.3381 target = 0.115401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.090001 restraints weight = 10530.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 1.85
r_work: 0.2938 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8328  Z= 0.087
  Angle     :  0.425  10.531  11348  Z= 0.214
  Chirality :  0.037   0.116   1356
  Planarity :  0.003   0.065   1398
  Dihedral  :  5.785  83.925   1230
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 20.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.26 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.27), residues: 1076
  helix:  2.77 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.29 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 380 
 HIS   0.001   0.000   HIS A 350 
 PHE   0.009   0.001   PHE A 166 
 TYR   0.006   0.001   TYR B 399 
 ARG   0.001   0.000   ARG A 291 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00259 (    2)
  link_NAG-ASN         : angle       2.04999 (    6)
  link_BETA1-4         : bond        0.00601 (    2)
  link_BETA1-4         : angle       3.28312 (    6)
  hydrogen bonds       : bond        0.03050 (  513)
  hydrogen bonds       : angle       3.96146 ( 1467)
  SS BOND              : bond        0.00056 (    8)
  SS BOND              : angle       1.07664 (   16)
  covalent geometry    : bond        0.00185 ( 8316)
  covalent geometry    : angle       0.41391 (11320)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7527 (ptt-90) cc_final: 0.7223 (ptt-90)
REVERT: A  470 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6749 (mtp)
REVERT: A  494 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8420 (mtp)
REVERT: B  103 ARG cc_start: 0.7471 (ptt-90) cc_final: 0.7191 (ptt-90)
REVERT: B  401 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.6759 (mpp)
REVERT: B  548 GLU cc_start: 0.7389 (tp30) cc_final: 0.6616 (mt-10)
  outliers start: 14
  outliers final: 8
  residues processed: 90
  average time/residue: 1.2243
  time to fit residues: 117.3676
Evaluate side-chains
  96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  388 TYR
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  470 MET
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain B residue  123 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  413 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 48 optimal weight:    0.0170
   chunk 78 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 72 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 64 optimal weight:    0.2980
   chunk 77 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    1.0622

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 163 ASN ** 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 = 0.3365 r_free = 0.3365 target = 0.114125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.089012 restraints weight = 10548.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 1.83
r_work: 0.2895 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2786 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8328  Z= 0.122
  Angle     :  0.451  10.800  11348  Z= 0.227
  Chirality :  0.037   0.116   1356
  Planarity :  0.004   0.065   1398
  Dihedral  :  5.494  75.438   1230
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 19.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.49 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.27), residues: 1076
  helix:  2.69 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.31 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 380 
 HIS   0.002   0.001   HIS B 541 
 PHE   0.010   0.001   PHE A 166 
 TYR   0.007   0.001   TYR B 399 
 ARG   0.001   0.000   ARG A 333 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    2)
  link_NAG-ASN         : angle       2.12388 (    6)
  link_BETA1-4         : bond        0.00448 (    2)
  link_BETA1-4         : angle       3.62234 (    6)
  hydrogen bonds       : bond        0.03318 (  513)
  hydrogen bonds       : angle       4.00411 ( 1467)
  SS BOND              : bond        0.00064 (    8)
  SS BOND              : angle       1.12886 (   16)
  covalent geometry    : bond        0.00272 ( 8316)
  covalent geometry    : angle       0.43908 (11320)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7501 (ptt-90) cc_final: 0.7198 (ptt-90)
REVERT: A  494 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8447 (mtp)
REVERT: B  103 ARG cc_start: 0.7463 (ptt-90) cc_final: 0.7184 (ptt-90)
REVERT: B  401 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.6732 (mpp)
REVERT: B  548 GLU cc_start: 0.7376 (tp30) cc_final: 0.6601 (mt-10)
  outliers start: 12
  outliers final: 8
  residues processed: 86
  average time/residue: 1.2592
  time to fit residues: 115.3110
Evaluate side-chains
  90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  123 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  413 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 35 optimal weight:    0.1980
   chunk 90 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 78 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    1.2388

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

Flipped N/Q/H residues before XYZ refinement:
** B 163 ASN ** 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 = 0.3352 r_free = 0.3352 target = 0.113249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.088042 restraints weight = 10711.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 1.85
r_work: 0.2894 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8328  Z= 0.131
  Angle     :  0.470  10.211  11348  Z= 0.236
  Chirality :  0.038   0.117   1356
  Planarity :  0.004   0.064   1398
  Dihedral  :  4.978  56.645   1230
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 19.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.14 %
    Favored  : 88.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.27), residues: 1076
  helix:  2.61 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.34 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 380 
 HIS   0.002   0.001   HIS B 541 
 PHE   0.012   0.001   PHE A 442 
 TYR   0.009   0.001   TYR B 399 
 ARG   0.001   0.000   ARG B 291 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00280 (    2)
  link_NAG-ASN         : angle       2.20967 (    6)
  link_BETA1-4         : bond        0.00213 (    2)
  link_BETA1-4         : angle       4.33921 (    6)
  hydrogen bonds       : bond        0.03483 (  513)
  hydrogen bonds       : angle       4.08361 ( 1467)
  SS BOND              : bond        0.00069 (    8)
  SS BOND              : angle       1.22110 (   16)
  covalent geometry    : bond        0.00294 ( 8316)
  covalent geometry    : angle       0.45447 (11320)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7474 (ptt-90) cc_final: 0.7176 (ptt-90)
REVERT: A  494 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8482 (mtp)
REVERT: B  103 ARG cc_start: 0.7415 (ptt-90) cc_final: 0.7141 (ptt-90)
REVERT: B  401 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.6667 (mpp)
REVERT: B  548 GLU cc_start: 0.7392 (tp30) cc_final: 0.6624 (mt-10)
  outliers start: 14
  outliers final: 9
  residues processed: 87
  average time/residue: 1.2799
  time to fit residues: 118.4159
Evaluate side-chains
  91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  388 TYR
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  123 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  413 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0870
   chunk 2 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 54 optimal weight:   10.0000
   chunk 101 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 100 optimal weight:    0.4980
   chunk 18 optimal weight:    0.5980
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 541 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.115534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.090183 restraints weight = 10440.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 1.84
r_work: 0.2937 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8328  Z= 0.081
  Angle     :  0.422   8.041  11348  Z= 0.212
  Chirality :  0.037   0.117   1356
  Planarity :  0.003   0.066   1398
  Dihedral  :  4.365  36.242   1230
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 21.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.61 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.27), residues: 1076
  helix:  2.81 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.26 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 482 
 HIS   0.001   0.000   HIS B 378 
 PHE   0.008   0.001   PHE A 166 
 TYR   0.006   0.001   TYR A 418 
 ARG   0.001   0.000   ARG B  42 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00263 (    2)
  link_NAG-ASN         : angle       2.21518 (    6)
  link_BETA1-4         : bond        0.00086 (    2)
  link_BETA1-4         : angle       4.55522 (    6)
  hydrogen bonds       : bond        0.02973 (  513)
  hydrogen bonds       : angle       3.94215 ( 1467)
  SS BOND              : bond        0.00077 (    8)
  SS BOND              : angle       1.13333 (   16)
  covalent geometry    : bond        0.00169 ( 8316)
  covalent geometry    : angle       0.40362 (11320)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7487 (ptt-90) cc_final: 0.7190 (ptt-90)
REVERT: B  103 ARG cc_start: 0.7424 (ptt-90) cc_final: 0.7112 (ptt-90)
REVERT: B  401 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.6615 (mpp)
REVERT: B  548 GLU cc_start: 0.7350 (tp30) cc_final: 0.6589 (mt-10)
  outliers start: 11
  outliers final: 9
  residues processed: 92
  average time/residue: 1.2076
  time to fit residues: 118.5267
Evaluate side-chains
  94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain A residue  388 TYR
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  123 CYS
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  413 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0000
   chunk 98 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 94 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
** B 163 ASN ** 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 = 0.3372 r_free = 0.3372 target = 0.114960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.089972 restraints weight = 10654.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.82
r_work: 0.2923 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8328  Z= 0.094
  Angle     :  0.423   7.873  11348  Z= 0.214
  Chirality :  0.037   0.116   1356
  Planarity :  0.003   0.065   1398
  Dihedral  :  4.257  31.635   1230
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 20.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.61 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.27), residues: 1076
  helix:  2.81 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.26 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 482 
 HIS   0.001   0.000   HIS A 364 
 PHE   0.009   0.001   PHE A 166 
 TYR   0.005   0.001   TYR B 399 
 ARG   0.001   0.000   ARG A 216 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00257 (    2)
  link_NAG-ASN         : angle       2.24471 (    6)
  link_BETA1-4         : bond        0.00077 (    2)
  link_BETA1-4         : angle       4.28900 (    6)
  hydrogen bonds       : bond        0.03075 (  513)
  hydrogen bonds       : angle       3.93704 ( 1467)
  SS BOND              : bond        0.00062 (    8)
  SS BOND              : angle       1.12679 (   16)
  covalent geometry    : bond        0.00202 ( 8316)
  covalent geometry    : angle       0.40686 (11320)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5589.89 seconds
wall clock time: 97 minutes 13.28 seconds (5833.28 seconds total)