Starting phenix.real_space_refine
on Mon Apr 28 23:35:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8irm_35679/04_2025/8irm_35679.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8irm_35679/04_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_35679/04_2025/8irm_35679.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8irm_35679/04_2025/8irm_35679.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8irm_35679/04_2025/8irm_35679.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8irm_35679/04_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.82, per 1000 atoms: 0.72
  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: 2.43
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.97
  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: 2.54

  Time building geometry restraints manager: 2.83 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: 0.05
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:             1.120
  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:             0.260
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.160
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  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:13.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.910
-------------------------------------------------------------------------------
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  : 2.593 
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: 1.7832
  time to fit residues: 190.2765
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  : 1.017 
-------------------------------------------------------------------------------
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 = 43)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.091410 restraints weight = 10542.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.82
r_work: 0.2955 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
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  : 1.015 
Fit side-chains
REVERT: B  548 GLU cc_start: 0.7401 (tp30) cc_final: 0.6695 (mt-10)
  outliers start: 9
  outliers final: 6
  residues processed: 92
  average time/residue: 1.5549
  time to fit residues: 152.1447
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  : 0.923 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 5 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 89 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.8542

-------------------------------------------------------------------------------
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 = 0.3370 r_free = 0.3370 target = 0.114676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.089895 restraints weight = 10680.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.80
r_work: 0.2935 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8328  Z= 0.110
  Angle     :  0.451   8.478  11348  Z= 0.232
  Chirality :  0.037   0.133   1356
  Planarity :  0.004   0.064   1398
  Dihedral  :  7.139 100.568   1230
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 18.67
  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:  2.05 (0.27), residues: 1076
  helix:  2.39 (0.20), residues: 666
  sheet: -4.68 (0.65), residues: 20
  loop : -0.08 (0.33), 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   0.019   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        0.00297 (    2)
  link_NAG-ASN         : angle       2.27518 (    6)
  link_BETA1-4         : bond        0.00604 (    2)
  link_BETA1-4         : angle       2.72305 (    6)
  hydrogen bonds       : bond        0.03631 (  513)
  hydrogen bonds       : angle       4.21783 ( 1467)
  SS BOND              : bond        0.00163 (    8)
  SS BOND              : angle       1.11857 (   16)
  covalent geometry    : bond        0.00236 ( 8316)
  covalent geometry    : angle       0.44194 (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
  100 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.970 
Fit side-chains
REVERT: B  401 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7157 (mtp)
REVERT: B  548 GLU cc_start: 0.7451 (tp30) cc_final: 0.6755 (mt-10)
  outliers start: 17
  outliers final: 7
  residues processed: 90
  average time/residue: 1.2621
  time to fit residues: 121.0219
Evaluate side-chains
  89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
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 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:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 6 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 96 optimal weight:    0.4980
   chunk 74 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3368 r_free = 0.3368 target = 0.114283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.089208 restraints weight = 10529.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 1.83
r_work: 0.2905 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8328  Z= 0.122
  Angle     :  0.454   8.815  11348  Z= 0.232
  Chirality :  0.038   0.134   1356
  Planarity :  0.004   0.065   1398
  Dihedral  :  6.794  98.181   1230
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 19.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  8.51 %
    Favored  : 89.51 %
  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:  2.11 (0.27), residues: 1076
  helix:  2.47 (0.20), residues: 666
  sheet: -4.83 (0.60), residues: 20
  loop : -0.12 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 380 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.015   0.001   PHE A 442 
 TYR   0.009   0.001   TYR B 399 
 ARG   0.001   0.000   ARG B  42 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00298 (    2)
  link_NAG-ASN         : angle       2.24816 (    6)
  link_BETA1-4         : bond        0.00452 (    2)
  link_BETA1-4         : angle       2.73267 (    6)
  hydrogen bonds       : bond        0.03487 (  513)
  hydrogen bonds       : angle       4.14832 ( 1467)
  SS BOND              : bond        0.00089 (    8)
  SS BOND              : angle       0.96510 (   16)
  covalent geometry    : bond        0.00268 ( 8316)
  covalent geometry    : angle       0.44534 (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
  99 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
REVERT: A  470 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6800 (mtp)
REVERT: A  494 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8436 (mtp)
REVERT: A  507 MET cc_start: 0.8819 (mmp) cc_final: 0.8573 (mmp)
REVERT: B  548 GLU cc_start: 0.7397 (tp30) cc_final: 0.6718 (mt-10)
  outliers start: 17
  outliers final: 7
  residues processed: 87
  average time/residue: 1.2846
  time to fit residues: 119.0318
Evaluate side-chains
  88 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
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  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:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3341 r_free = 0.3341 target = 0.112256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.087106 restraints weight = 10509.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.83
r_work: 0.2880 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8328  Z= 0.158
  Angle     :  0.490   9.713  11348  Z= 0.250
  Chirality :  0.039   0.133   1356
  Planarity :  0.004   0.063   1398
  Dihedral  :  6.509  93.267   1230
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 18.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  9.21 %
    Favored  : 88.81 %
  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:  1.99 (0.26), residues: 1076
  helix:  2.39 (0.20), residues: 666
  sheet: -4.84 (0.59), residues: 20
  loop : -0.21 (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 A 364 
 PHE   0.017   0.002   PHE A 442 
 TYR   0.010   0.001   TYR B 399 
 ARG   0.001   0.000   ARG A 508 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00306 (    2)
  link_NAG-ASN         : angle       2.32210 (    6)
  link_BETA1-4         : bond        0.00553 (    2)
  link_BETA1-4         : angle       2.98603 (    6)
  hydrogen bonds       : bond        0.03800 (  513)
  hydrogen bonds       : angle       4.20502 ( 1467)
  SS BOND              : bond        0.00127 (    8)
  SS BOND              : angle       1.37222 (   16)
  covalent geometry    : bond        0.00364 ( 8316)
  covalent geometry    : angle       0.48008 (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
  94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7472 (ptt-90) cc_final: 0.7163 (ptt-90)
REVERT: A  401 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7228 (mpp)
REVERT: A  470 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6976 (mtp)
REVERT: A  494 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8502 (mtp)
REVERT: B  103 ARG cc_start: 0.7406 (ptt-90) cc_final: 0.7066 (ptt-90)
REVERT: B  401 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.6851 (mpp)
REVERT: B  548 GLU cc_start: 0.7401 (tp30) cc_final: 0.6599 (mt-10)
  outliers start: 17
  outliers final: 10
  residues processed: 85
  average time/residue: 1.2990
  time to fit residues: 117.8601
Evaluate side-chains
  89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
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  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:    0.1980
   chunk 65 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 76 optimal weight:    4.9990
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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 = 0.3360 r_free = 0.3360 target = 0.113771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.088176 restraints weight = 10463.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 1.86
r_work: 0.2916 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8328  Z= 0.099
  Angle     :  0.440  10.027  11348  Z= 0.223
  Chirality :  0.037   0.123   1356
  Planarity :  0.004   0.065   1398
  Dihedral  :  6.185  89.951   1230
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 19.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  9.44 %
    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:  2.24 (0.27), residues: 1076
  helix:  2.59 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.40 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 380 
 HIS   0.001   0.000   HIS A 350 
 PHE   0.009   0.001   PHE A 166 
 TYR   0.007   0.001   TYR B 399 
 ARG   0.001   0.000   ARG B  51 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00276 (    2)
  link_NAG-ASN         : angle       2.14018 (    6)
  link_BETA1-4         : bond        0.00576 (    2)
  link_BETA1-4         : angle       3.09516 (    6)
  hydrogen bonds       : bond        0.03275 (  513)
  hydrogen bonds       : angle       4.06573 ( 1467)
  SS BOND              : bond        0.00056 (    8)
  SS BOND              : angle       1.15081 (   16)
  covalent geometry    : bond        0.00211 ( 8316)
  covalent geometry    : angle       0.42969 (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
  99 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7495 (ptt-90) cc_final: 0.7199 (ptt-90)
REVERT: A  470 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6885 (mtp)
REVERT: A  494 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8465 (mtp)
REVERT: B  103 ARG cc_start: 0.7385 (ptt-90) cc_final: 0.7117 (ptt-90)
REVERT: B  401 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.6798 (mpp)
REVERT: B  548 GLU cc_start: 0.7394 (tp30) cc_final: 0.6595 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 90
  average time/residue: 1.2088
  time to fit residues: 116.1000
Evaluate side-chains
  94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
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  439 VAL
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
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   chunk 96 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 = 0.3306 r_free = 0.3306 target = 0.110203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.084582 restraints weight = 10530.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 1.86
r_work: 0.2834 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8328  Z= 0.174
  Angle     :  0.499  10.503  11348  Z= 0.253
  Chirality :  0.039   0.119   1356
  Planarity :  0.004   0.063   1398
  Dihedral  :  6.040  83.522   1230
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 18.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  9.67 %
    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:  2.00 (0.26), residues: 1076
  helix:  2.39 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.49 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 380 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.015   0.002   PHE A 442 
 TYR   0.010   0.001   TYR B 399 
 ARG   0.001   0.000   ARG A 508 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00304 (    2)
  link_NAG-ASN         : angle       2.29493 (    6)
  link_BETA1-4         : bond        0.00525 (    2)
  link_BETA1-4         : angle       3.39182 (    6)
  hydrogen bonds       : bond        0.03820 (  513)
  hydrogen bonds       : angle       4.19899 ( 1467)
  SS BOND              : bond        0.00094 (    8)
  SS BOND              : angle       1.31194 (   16)
  covalent geometry    : bond        0.00401 ( 8316)
  covalent geometry    : angle       0.48857 (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
  94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7441 (ptt-90) cc_final: 0.7137 (ptt-90)
REVERT: A  470 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6938 (mtp)
REVERT: A  494 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8514 (mtp)
REVERT: B  103 ARG cc_start: 0.7358 (ptt-90) cc_final: 0.7057 (ptt-90)
REVERT: B  401 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.6680 (mpp)
REVERT: B  548 GLU cc_start: 0.7373 (tp30) cc_final: 0.6568 (mt-10)
  outliers start: 16
  outliers final: 11
  residues processed: 86
  average time/residue: 1.2393
  time to fit residues: 114.1047
Evaluate side-chains
  92 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
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  388 TYR
Chi-restraints excluded: chain A residue  439 VAL
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
Chi-restraints excluded: chain B residue  468 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 78 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   chunk 64 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0470
   chunk 102 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.7278

-------------------------------------------------------------------------------
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 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 = 0.3348 r_free = 0.3348 target = 0.113301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.087344 restraints weight = 10393.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.89
r_work: 0.2878 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8328  Z= 0.096
  Angle     :  0.445  10.798  11348  Z= 0.223
  Chirality :  0.037   0.116   1356
  Planarity :  0.004   0.064   1398
  Dihedral  :  5.564  76.186   1230
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 20.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  9.79 %
    Favored  : 88.58 %
  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:  2.26 (0.27), residues: 1076
  helix:  2.61 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.41 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 380 
 HIS   0.001   0.000   HIS A 364 
 PHE   0.010   0.001   PHE A 166 
 TYR   0.006   0.001   TYR B 399 
 ARG   0.001   0.000   ARG B 291 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00255 (    2)
  link_NAG-ASN         : angle       2.15432 (    6)
  link_BETA1-4         : bond        0.00445 (    2)
  link_BETA1-4         : angle       3.68175 (    6)
  hydrogen bonds       : bond        0.03227 (  513)
  hydrogen bonds       : angle       4.04802 ( 1467)
  SS BOND              : bond        0.00058 (    8)
  SS BOND              : angle       1.21095 (   16)
  covalent geometry    : bond        0.00205 ( 8316)
  covalent geometry    : angle       0.43202 (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
  94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7445 (ptt-90) cc_final: 0.7154 (ptt-90)
REVERT: A  470 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6840 (mtp)
REVERT: A  494 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8484 (mtp)
REVERT: B  103 ARG cc_start: 0.7349 (ptt-90) cc_final: 0.7056 (ptt-90)
REVERT: B  401 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.6686 (mpp)
REVERT: B  548 GLU cc_start: 0.7366 (tp30) cc_final: 0.6593 (mt-10)
  outliers start: 14
  outliers final: 10
  residues processed: 86
  average time/residue: 1.4257
  time to fit residues: 130.1708
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  : 0.831 
-------------------------------------------------------------------------------
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  439 VAL
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
Chi-restraints excluded: chain B residue  468 LEU
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:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 84 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
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 = 0.3280 r_free = 0.3280 target = 0.108216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.082146 restraints weight = 10613.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 1.89
r_work: 0.2796 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2683 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   8328  Z= 0.257
  Angle     :  0.566  10.575  11348  Z= 0.287
  Chirality :  0.042   0.121   1356
  Planarity :  0.004   0.062   1398
  Dihedral  :  5.578  65.638   1230
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 17.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  9.79 %
    Favored  : 88.58 %
  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:  1.72 (0.26), residues: 1076
  helix:  2.14 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.55 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 380 
 HIS   0.003   0.001   HIS B 364 
 PHE   0.020   0.002   PHE A 442 
 TYR   0.012   0.001   TYR B 399 
 ARG   0.002   0.000   ARG B 291 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00342 (    2)
  link_NAG-ASN         : angle       2.49199 (    6)
  link_BETA1-4         : bond        0.00288 (    2)
  link_BETA1-4         : angle       4.18320 (    6)
  hydrogen bonds       : bond        0.04308 (  513)
  hydrogen bonds       : angle       4.35514 ( 1467)
  SS BOND              : bond        0.00128 (    8)
  SS BOND              : angle       1.53972 (   16)
  covalent geometry    : bond        0.00596 ( 8316)
  covalent geometry    : angle       0.55237 (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
  87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7384 (ptt-90) cc_final: 0.7046 (ptt-90)
REVERT: A  470 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6966 (mtp)
REVERT: A  494 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8564 (mtp)
REVERT: B  103 ARG cc_start: 0.7332 (ptt-90) cc_final: 0.7052 (ptt-90)
REVERT: B  401 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.6687 (mpp)
REVERT: B  548 GLU cc_start: 0.7393 (tp30) cc_final: 0.6584 (mt-10)
  outliers start: 14
  outliers final: 9
  residues processed: 81
  average time/residue: 1.5016
  time to fit residues: 129.3419
Evaluate side-chains
  85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
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  365 THR
Chi-restraints excluded: chain A residue  388 TYR
Chi-restraints excluded: chain A residue  439 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 101 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 18 optimal weight:    0.2980
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 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 = 0.3336 r_free = 0.3336 target = 0.112335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.086509 restraints weight = 10343.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 1.88
r_work: 0.2869 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8328  Z= 0.102
  Angle     :  0.459   9.967  11348  Z= 0.229
  Chirality :  0.037   0.118   1356
  Planarity :  0.004   0.063   1398
  Dihedral  :  4.923  52.271   1230
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 20.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  9.91 %
    Favored  : 88.81 %
  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:  2.11 (0.26), residues: 1076
  helix:  2.49 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.46 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 380 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.009   0.001   PHE A 166 
 TYR   0.007   0.001   TYR B 399 
 ARG   0.001   0.000   ARG B 508 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00244 (    2)
  link_NAG-ASN         : angle       2.27643 (    6)
  link_BETA1-4         : bond        0.00189 (    2)
  link_BETA1-4         : angle       4.52658 (    6)
  hydrogen bonds       : bond        0.03328 (  513)
  hydrogen bonds       : angle       4.10040 ( 1467)
  SS BOND              : bond        0.00065 (    8)
  SS BOND              : angle       1.31734 (   16)
  covalent geometry    : bond        0.00220 ( 8316)
  covalent geometry    : angle       0.44164 (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
  89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 ARG cc_start: 0.7390 (ptt-90) cc_final: 0.7120 (ptt-90)
REVERT: A  470 MET cc_start: 0.7083 (ttp) cc_final: 0.6839 (mtp)
REVERT: A  494 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8527 (mtp)
REVERT: B  103 ARG cc_start: 0.7329 (ptt-90) cc_final: 0.7048 (ptt-90)
REVERT: B  401 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.6645 (mpp)
REVERT: B  548 GLU cc_start: 0.7378 (tp30) cc_final: 0.6575 (mt-10)
  outliers start: 11
  outliers final: 8
  residues processed: 83
  average time/residue: 1.2039
  time to fit residues: 106.4707
Evaluate side-chains
  88 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
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  439 VAL
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  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:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 94 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 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 = 0.3341 r_free = 0.3341 target = 0.112808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.086937 restraints weight = 10450.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 1.89
r_work: 0.2875 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.1954

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= 0.106
  Angle     :  0.446   8.582  11348  Z= 0.225
  Chirality :  0.037   0.116   1356
  Planarity :  0.004   0.063   1398
  Dihedral  :  4.529  35.403   1230
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 20.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 10.02 %
    Favored  : 88.69 %
  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:  2.61 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.38 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 482 
 HIS   0.001   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 216 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00262 (    2)
  link_NAG-ASN         : angle       2.32370 (    6)
  link_BETA1-4         : bond        0.00108 (    2)
  link_BETA1-4         : angle       4.58737 (    6)
  hydrogen bonds       : bond        0.03243 (  513)
  hydrogen bonds       : angle       4.04377 ( 1467)
  SS BOND              : bond        0.00064 (    8)
  SS BOND              : angle       1.20227 (   16)
  covalent geometry    : bond        0.00233 ( 8316)
  covalent geometry    : angle       0.42817 (11320)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6258.47 seconds
wall clock time: 110 minutes 42.12 seconds (6642.12 seconds total)