Starting phenix.real_space_refine
on Sun May 18 00:43:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wmq_37658/05_2025/8wmq_37658_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wmq_37658/05_2025/8wmq_37658.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wmq_37658/05_2025/8wmq_37658.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wmq_37658/05_2025/8wmq_37658.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wmq_37658/05_2025/8wmq_37658_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wmq_37658/05_2025/8wmq_37658_trim.cif"
  }
  resolution = 3.3
  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=   0.003
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    5300      2.51       5
     N    1316      2.21       5
     O    1472      1.98       5
     H    8208      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 16348
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 8130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 8130
          Classifications: {'peptide': 540}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516}
    Chain: "A"
      Number of atoms: 8130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 8130
          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: "B"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 16
          Unusual residues: {'ZEA': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 16
          Unusual residues: {'ZEA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.02, per 1000 atoms: 0.49
  Number of scatterers: 16348
  At special positions: 0
  Unit cell: (96.163, 114.885, 101.269, 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    5300      6.00
     H    8208      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    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=2.04
    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
    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

  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: 4.34
  Conformation dependent library (CDL) restraints added in 1.4 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:
      52 helices and 8 sheets defined
      67.5% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'B' and resid 19 through 30
    Processing helix  chain 'B' and resid 31 through 37
    Processing helix  chain 'B' and resid 39 through 43
    Processing helix  chain 'B' and resid 46 through 61
    Processing helix  chain 'B' and resid 62 through 73
      removed outlier: 4.203A  pdb=" N   ALA B  68 " --> pdb=" O   LEU B  64 " (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
    Processing helix  chain 'B' and resid 159 through 169
      removed outlier: 3.760A  pdb=" N   ALA B 164 " --> pdb=" O   MET B 160 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   TYR B 165 " --> pdb=" O   GLY B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 201
      removed outlier: 3.542A  pdb=" N   ILE B 201 " --> pdb=" O   PHE B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 209
    Processing helix  chain 'B' and resid 212 through 232
      removed outlier: 4.510A  pdb=" N   SER B 220 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
      removed outlier: 4.480A  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
      removed outlier: 3.509A  pdb=" N   TRP B 298 " --> pdb=" O   SER B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 331
    Processing helix  chain 'B' and resid 343 through 355
      removed outlier: 3.861A  pdb=" N   LYS B 355 " --> pdb=" O   ASP B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 405
      removed outlier: 3.728A  pdb=" N   TRP B 380 " --> pdb=" O   LYS B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 435
    Processing helix  chain 'B' and resid 444 through 451
      removed outlier: 4.268A  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: 4.000A  pdb=" N   THR B 500 " --> pdb=" O   LYS B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 524
      Proline residue:  B 512  - end of helix
      removed outlier: 3.637A  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 554
      removed outlier: 5.159A  pdb=" N   TRP B 543 " --> pdb=" O   VAL B 539 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   ASP B 544 " --> pdb=" O   LEU B 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 30
    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 60
    Processing helix  chain 'A' and resid 62 through 73
      removed outlier: 4.200A  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
      removed outlier: 3.862A  pdb=" N   ALA A 164 " --> pdb=" O   MET A 160 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   TYR A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 202
    Processing helix  chain 'A' and resid 203 through 211
      removed outlier: 3.852A  pdb=" N   VAL A 211 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 232
      removed outlier: 4.510A  pdb=" N   SER A 220 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 4.499A  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 330
    Processing helix  chain 'A' and resid 343 through 355
      removed outlier: 3.862A  pdb=" N   LYS A 355 " --> pdb=" O   ASP A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 406
      removed outlier: 3.735A  pdb=" N   TRP A 380 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 435
    Processing helix  chain 'A' and resid 445 through 451
    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
    Processing helix  chain 'A' and resid 497 through 502
      removed outlier: 4.006A  pdb=" N   THR A 500 " --> pdb=" O   LYS A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 524
      Proline residue:  A 512  - end of helix
      removed outlier: 3.634A  pdb=" N   MET A 520 " --> pdb=" O   THR A 516 " (cutoff:3.500A)
      Proline residue:  A 521  - end of helix
    Processing helix  chain 'A' and resid 525 through 554
      removed outlier: 3.543A  pdb=" N   GLY A 529 " --> pdb=" O   SER A 525 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   TRP A 543 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
      removed outlier: 5.150A  pdb=" N   ASP A 544 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 86 through 87
    Processing sheet with id=AA2, first strand: chain 'B' and resid 156 through 158
    Processing sheet with id=AA3, first strand: chain 'B' and resid 241 through 242
      removed outlier: 3.664A  pdb=" N   THR B 250 " --> pdb=" O   GLY B 242 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 274 through 275
      removed outlier: 3.766A  pdb=" N   SER B 274 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   SER B 261 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   SER A 261 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   SER A 274 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 287
      removed outlier: 4.104A  pdb=" N   SER B 261 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   SER A 261 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 158
    Processing sheet with id=AA8, first strand: chain 'A' and resid 241 through 242

    513 hydrogen bonds defined for protein.
    1458 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: 5.33

  Time building geometry restraints manager: 5.14 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8204
        1.03 -     1.23: 14
        1.23 -     1.42: 3414
        1.42 -     1.62: 4820
        1.62 -     1.81: 84
  Bond restraints: 16536
  Sorted by residual:
  bond pdb=" C6  ZEA A 701 "
       pdb=" N10 ZEA A 701 "
    ideal  model  delta    sigma   weight residual
    1.336  1.466 -0.130 2.00e-02 2.50e+03 4.21e+01
  bond pdb=" C6  ZEA B 701 "
       pdb=" N10 ZEA B 701 "
    ideal  model  delta    sigma   weight residual
    1.336  1.466 -0.130 2.00e-02 2.50e+03 4.20e+01
  bond pdb=" C13 ZEA A 701 "
       pdb=" C14 ZEA A 701 "
    ideal  model  delta    sigma   weight residual
    1.502  1.596 -0.094 2.00e-02 2.50e+03 2.22e+01
  bond pdb=" C13 ZEA B 701 "
       pdb=" C14 ZEA B 701 "
    ideal  model  delta    sigma   weight residual
    1.502  1.596 -0.094 2.00e-02 2.50e+03 2.21e+01
  bond pdb=" C13 ZEA A 701 "
       pdb=" C15 ZEA A 701 "
    ideal  model  delta    sigma   weight residual
    1.500  1.557 -0.057 2.00e-02 2.50e+03 8.08e+00
  ... (remaining 16531 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.39: 29912
        8.39 -    16.79: 4
       16.79 -    25.18: 0
       25.18 -    33.58: 2
       33.58 -    41.97: 4
  Bond angle restraints: 29922
  Sorted by residual:
  angle pdb=" C12 ZEA B 701 "
        pdb=" C13 ZEA B 701 "
        pdb=" C15 ZEA B 701 "
      ideal   model   delta    sigma   weight residual
     125.58  167.55  -41.97 3.00e+00 1.11e-01 1.96e+02
  angle pdb=" C12 ZEA A 701 "
        pdb=" C13 ZEA A 701 "
        pdb=" C15 ZEA A 701 "
      ideal   model   delta    sigma   weight residual
     125.58  167.55  -41.97 3.00e+00 1.11e-01 1.96e+02
  angle pdb=" C12 ZEA B 701 "
        pdb=" C13 ZEA B 701 "
        pdb=" C14 ZEA B 701 "
      ideal   model   delta    sigma   weight residual
     121.92   87.91   34.01 3.00e+00 1.11e-01 1.28e+02
  angle pdb=" C12 ZEA A 701 "
        pdb=" C13 ZEA A 701 "
        pdb=" C14 ZEA A 701 "
      ideal   model   delta    sigma   weight residual
     121.92   87.94   33.98 3.00e+00 1.11e-01 1.28e+02
  angle pdb=" C14 ZEA A 701 "
        pdb=" C13 ZEA A 701 "
        pdb=" C15 ZEA A 701 "
      ideal   model   delta    sigma   weight residual
     112.50   79.62   32.88 3.00e+00 1.11e-01 1.20e+02
  ... (remaining 29917 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.94: 7404
       24.94 -    49.87: 339
       49.87 -    74.80: 132
       74.80 -    99.74: 4
       99.74 -   124.67: 3
  Dihedral angle restraints: 7882
    sinusoidal: 4248
      harmonic: 3634
  Sorted by residual:
  dihedral pdb=" CB  CYS A  78 "
           pdb=" SG  CYS A  78 "
           pdb=" SG  CYS A 123 "
           pdb=" CB  CYS A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -145.94   59.94     1      1.00e+01 1.00e-02 4.79e+01
  dihedral pdb=" CB  CYS B  78 "
           pdb=" SG  CYS B  78 "
           pdb=" SG  CYS B 123 "
           pdb=" CB  CYS B 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -144.84   58.84     1      1.00e+01 1.00e-02 4.63e+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  150.51   29.49     0      5.00e+00 4.00e-02 3.48e+01
  ... (remaining 7879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1137
       0.053 -    0.105: 191
       0.105 -    0.158: 27
       0.158 -    0.210: 0
       0.210 -    0.263: 1
  Chirality restraints: 1356
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN B 270 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CA  ILE A 362 "
            pdb=" N   ILE A 362 "
            pdb=" C   ILE A 362 "
            pdb=" CB  ILE A 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.90e-01
  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    2.42    0.13 2.00e-01 2.50e+01 4.38e-01
  ... (remaining 1353 not shown)

  Planarity restraints: 2434
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 486 "   -0.043 5.00e-02 4.00e+02   6.49e-02 6.74e+00
        pdb=" N   PRO A 487 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 487 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 487 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 486 "   -0.043 5.00e-02 4.00e+02   6.46e-02 6.68e+00
        pdb=" N   PRO B 487 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B 487 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 487 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 340 "    0.043 5.00e-02 4.00e+02   6.32e-02 6.39e+00
        pdb=" N   PRO A 341 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 341 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 341 "    0.035 5.00e-02 4.00e+02
  ... (remaining 2431 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 766
        2.19 -     2.79: 32112
        2.79 -     3.39: 45274
        3.39 -     4.00: 56801
        4.00 -     4.60: 89965
  Nonbonded interactions: 224918
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 519 "
            pdb=" HG1 THR A 523 "
     model   vdw
     1.583 2.450
  nonbonded pdb=" O   LEU B 519 "
            pdb=" HG1 THR B 523 "
     model   vdw
     1.584 2.450
  nonbonded pdb=" HG  SER A 268 "
            pdb=" OD1 ASN A 270 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" O   SER B  88 "
            pdb="HD21 ASN A 270 "
     model   vdw
     1.630 2.450
  nonbonded pdb=" O   PHE B 332 "
            pdb=" HG1 THR B 338 "
     model   vdw
     1.633 2.450
  ... (remaining 224913 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:             0.840
  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:             0.280
  Extract box with map and model:          0.610
  Check model and map are aligned:         0.120
  Set scattering table:                    0.140
  Process input model:                     35.060
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
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      :  0.004   0.130   8340  Z= 0.213
  Angle     :  1.070  41.971  11362  Z= 0.456
  Chirality :  0.040   0.263   1356
  Planarity :  0.005   0.065   1400
  Dihedral  : 14.040 124.675   2938
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.26), residues: 1076
  helix:  1.65 (0.21), residues: 642
  sheet:  None (None), residues: 0
  loop : -1.07 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 482 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.013   0.001   TYR B 309 
 ARG   0.017   0.001   ARG B  23 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00177 (    2)
  link_NAG-ASN         : angle       1.42070 (    6)
  link_BETA1-4         : bond        0.00262 (    2)
  link_BETA1-4         : angle       1.54546 (    6)
  hydrogen bonds       : bond        0.13654 (  509)
  hydrogen bonds       : angle       5.56263 ( 1458)
  SS BOND              : bond        0.00223 (    8)
  SS BOND              : angle       0.74306 (   16)
  covalent geometry    : bond        0.00430 ( 8328)
  covalent geometry    : angle       1.07007 (11334)

*********************** 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
  132 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 1.292 
Fit side-chains
REVERT: B  390 ASP cc_start: 0.7078 (m-30) cc_final: 0.6821 (m-30)
REVERT: B  444 GLU cc_start: 0.6848 (mp0) cc_final: 0.6634 (mp0)
REVERT: A  390 ASP cc_start: 0.7144 (m-30) cc_final: 0.6882 (m-30)
REVERT: A  444 GLU cc_start: 0.6869 (mp0) cc_final: 0.6630 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.2753
  time to fit residues: 57.3236
Evaluate side-chains
  108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    0.2980
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.3784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.123146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.100220 restraints weight = 39667.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.48
r_work: 0.3253 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.0972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8340  Z= 0.132
  Angle     :  0.997  37.239  11362  Z= 0.405
  Chirality :  0.039   0.206   1356
  Planarity :  0.005   0.065   1400
  Dihedral  :  8.548 110.840   1236
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  6.18 %
    Favored  : 93.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.26), residues: 1076
  helix:  1.82 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.90 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 482 
 HIS   0.004   0.001   HIS B 360 
 PHE   0.012   0.001   PHE A 466 
 TYR   0.010   0.001   TYR B 524 
 ARG   0.004   0.000   ARG A  23 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00473 (    2)
  link_NAG-ASN         : angle       1.66844 (    6)
  link_BETA1-4         : bond        0.00274 (    2)
  link_BETA1-4         : angle       2.54541 (    6)
  hydrogen bonds       : bond        0.05758 (  509)
  hydrogen bonds       : angle       4.63479 ( 1458)
  SS BOND              : bond        0.00121 (    8)
  SS BOND              : angle       0.78063 (   16)
  covalent geometry    : bond        0.00277 ( 8328)
  covalent geometry    : angle       0.99583 (11334)

*********************** 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
  118 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 114
  time to evaluate  : 1.193 
Fit side-chains
REVERT: B  390 ASP cc_start: 0.7565 (m-30) cc_final: 0.7276 (m-30)
REVERT: B  444 GLU cc_start: 0.7498 (mp0) cc_final: 0.7222 (mp0)
REVERT: A  390 ASP cc_start: 0.7568 (m-30) cc_final: 0.7288 (m-30)
  outliers start: 4
  outliers final: 3
  residues processed: 116
  average time/residue: 0.2941
  time to fit residues: 52.9484
Evaluate side-chains
  110 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 107
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain A residue  335 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 88 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   chunk 11 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    3.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.117178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.094642 restraints weight = 40519.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 2.46
r_work: 0.3171 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   8340  Z= 0.254
  Angle     :  1.047  37.898  11362  Z= 0.443
  Chirality :  0.043   0.210   1356
  Planarity :  0.006   0.069   1400
  Dihedral  :  8.448 104.530   1236
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.93 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  8.51 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.25), residues: 1076
  helix:  1.47 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.29 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 543 
 HIS   0.004   0.002   HIS B 350 
 PHE   0.020   0.002   PHE B 189 
 TYR   0.010   0.001   TYR B 524 
 ARG   0.001   0.000   ARG B 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00460 (    2)
  link_NAG-ASN         : angle       2.05379 (    6)
  link_BETA1-4         : bond        0.00099 (    2)
  link_BETA1-4         : angle       2.49400 (    6)
  hydrogen bonds       : bond        0.06771 (  509)
  hydrogen bonds       : angle       4.78521 ( 1458)
  SS BOND              : bond        0.00261 (    8)
  SS BOND              : angle       1.48597 (   16)
  covalent geometry    : bond        0.00580 ( 8328)
  covalent geometry    : angle       1.04408 (11334)

*********************** 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
  117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 1.170 
Fit side-chains
REVERT: B  390 ASP cc_start: 0.7639 (m-30) cc_final: 0.7400 (m-30)
REVERT: A   86 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7707 (mm)
  outliers start: 14
  outliers final: 11
  residues processed: 110
  average time/residue: 0.3134
  time to fit residues: 51.9011
Evaluate side-chains
  112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  347 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  394 THR
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  551 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    1.9586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.119393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.096929 restraints weight = 39961.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.45
r_work: 0.3204 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8340  Z= 0.144
  Angle     :  0.998  36.851  11362  Z= 0.404
  Chirality :  0.040   0.215   1356
  Planarity :  0.005   0.067   1400
  Dihedral  :  8.044  98.540   1236
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.67 %
    Favored  : 89.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.26), residues: 1076
  helix:  1.74 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.08 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 482 
 HIS   0.002   0.001   HIS A 289 
 PHE   0.014   0.001   PHE B 189 
 TYR   0.009   0.001   TYR B 524 
 ARG   0.001   0.000   ARG B 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00451 (    2)
  link_NAG-ASN         : angle       1.92380 (    6)
  link_BETA1-4         : bond        0.00333 (    2)
  link_BETA1-4         : angle       2.49331 (    6)
  hydrogen bonds       : bond        0.05735 (  509)
  hydrogen bonds       : angle       4.46237 ( 1458)
  SS BOND              : bond        0.00182 (    8)
  SS BOND              : angle       1.00799 (   16)
  covalent geometry    : bond        0.00311 ( 8328)
  covalent geometry    : angle       0.99546 (11334)

*********************** 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
  111 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 1.163 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 108
  average time/residue: 0.3059
  time to fit residues: 50.6224
Evaluate side-chains
  110 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  551 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0070
   chunk 68 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    2.0006

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.119402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.096996 restraints weight = 40586.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.47
r_work: 0.3202 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8340  Z= 0.149
  Angle     :  0.995  36.774  11362  Z= 0.400
  Chirality :  0.040   0.211   1356
  Planarity :  0.005   0.067   1400
  Dihedral  :  7.708  91.330   1236
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.84 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.26), residues: 1076
  helix:  1.87 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.05 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 482 
 HIS   0.002   0.001   HIS B 350 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.008   0.001   TYR B 524 
 ARG   0.001   0.000   ARG B 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00399 (    2)
  link_NAG-ASN         : angle       1.76247 (    6)
  link_BETA1-4         : bond        0.00275 (    2)
  link_BETA1-4         : angle       2.62802 (    6)
  hydrogen bonds       : bond        0.05498 (  509)
  hydrogen bonds       : angle       4.34737 ( 1458)
  SS BOND              : bond        0.00228 (    8)
  SS BOND              : angle       1.10507 (   16)
  covalent geometry    : bond        0.00328 ( 8328)
  covalent geometry    : angle       0.99254 (11334)

*********************** 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
  112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 1.309 
Fit side-chains
REVERT: B  524 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.7995 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 109
  average time/residue: 0.3164
  time to fit residues: 52.7053
Evaluate side-chains
  108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  347 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  524 TYR
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  551 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.7186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.119629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.097456 restraints weight = 39892.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.44
r_work: 0.3209 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8340  Z= 0.132
  Angle     :  0.987  36.566  11362  Z= 0.394
  Chirality :  0.039   0.208   1356
  Planarity :  0.005   0.067   1400
  Dihedral  :  7.457  85.713   1236
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.31 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.26), residues: 1076
  helix:  1.96 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.99 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 482 
 HIS   0.002   0.001   HIS B 289 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.009   0.001   TYR A 181 
 ARG   0.001   0.000   ARG B 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00396 (    2)
  link_NAG-ASN         : angle       1.71264 (    6)
  link_BETA1-4         : bond        0.00326 (    2)
  link_BETA1-4         : angle       2.76625 (    6)
  hydrogen bonds       : bond        0.05269 (  509)
  hydrogen bonds       : angle       4.24919 ( 1458)
  SS BOND              : bond        0.00188 (    8)
  SS BOND              : angle       0.98590 (   16)
  covalent geometry    : bond        0.00283 ( 8328)
  covalent geometry    : angle       0.98507 (11334)

*********************** 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
  112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  524 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.8083 (m-80)
  outliers start: 12
  outliers final: 10
  residues processed: 109
  average time/residue: 0.3400
  time to fit residues: 55.5673
Evaluate side-chains
  111 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  309 TYR
Chi-restraints excluded: chain B residue  347 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  524 TYR
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  551 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 33 optimal weight:    0.3980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 87 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A 235 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 = 0.3626 r_free = 0.3626 target = 0.118887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.096722 restraints weight = 40139.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.44
r_work: 0.3200 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8340  Z= 0.147
  Angle     :  0.994  36.537  11362  Z= 0.398
  Chirality :  0.039   0.208   1356
  Planarity :  0.005   0.066   1400
  Dihedral  :  7.228  78.238   1236
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.00 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.26), residues: 1076
  helix:  1.95 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.01 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 482 
 HIS   0.002   0.001   HIS A 350 
 PHE   0.020   0.001   PHE A 555 
 TYR   0.009   0.001   TYR A 181 
 ARG   0.001   0.000   ARG A 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00396 (    2)
  link_NAG-ASN         : angle       1.69609 (    6)
  link_BETA1-4         : bond        0.00193 (    2)
  link_BETA1-4         : angle       2.99714 (    6)
  hydrogen bonds       : bond        0.05351 (  509)
  hydrogen bonds       : angle       4.24393 ( 1458)
  SS BOND              : bond        0.00202 (    8)
  SS BOND              : angle       1.05190 (   16)
  covalent geometry    : bond        0.00322 ( 8328)
  covalent geometry    : angle       0.99133 (11334)

*********************** 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
  113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  524 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8065 (m-80)
  outliers start: 13
  outliers final: 12
  residues processed: 109
  average time/residue: 0.3521
  time to fit residues: 56.0708
Evaluate side-chains
  112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  309 TYR
Chi-restraints excluded: chain B residue  347 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  524 TYR
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  553 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 48 optimal weight:    4.9990
   chunk 92 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 235 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 = 0.3616 r_free = 0.3616 target = 0.117786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.095833 restraints weight = 40024.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.42
r_work: 0.3191 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8340  Z= 0.149
  Angle     :  0.998  36.648  11362  Z= 0.400
  Chirality :  0.040   0.204   1356
  Planarity :  0.005   0.067   1400
  Dihedral  :  6.769  65.621   1236
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.59 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.26), residues: 1076
  helix:  1.98 (0.20), residues: 646
  sheet:  None (None), residues: 0
  loop : -1.01 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 482 
 HIS   0.002   0.001   HIS A 289 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.009   0.001   TYR A 181 
 ARG   0.001   0.000   ARG A  42 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00391 (    2)
  link_NAG-ASN         : angle       1.76058 (    6)
  link_BETA1-4         : bond        0.00119 (    2)
  link_BETA1-4         : angle       3.56046 (    6)
  hydrogen bonds       : bond        0.05400 (  509)
  hydrogen bonds       : angle       4.22015 ( 1458)
  SS BOND              : bond        0.00188 (    8)
  SS BOND              : angle       1.07753 (   16)
  covalent geometry    : bond        0.00329 ( 8328)
  covalent geometry    : angle       0.99393 (11334)

*********************** 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
  115 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 1.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  524 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.8135 (m-80)
  outliers start: 13
  outliers final: 12
  residues processed: 111
  average time/residue: 0.3479
  time to fit residues: 57.1329
Evaluate side-chains
  114 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  309 TYR
Chi-restraints excluded: chain B residue  347 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  393 ASP
Chi-restraints excluded: chain B residue  524 TYR
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  553 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 33 optimal weight:    0.2980
   chunk 69 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 83 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 88 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 235 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 = 0.3649 r_free = 0.3649 target = 0.120343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.098449 restraints weight = 39814.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.41
r_work: 0.3229 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8340  Z= 0.108
  Angle     :  0.981  36.415  11362  Z= 0.385
  Chirality :  0.039   0.198   1356
  Planarity :  0.005   0.066   1400
  Dihedral  :  5.880  52.895   1236
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.70 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.27), residues: 1076
  helix:  2.21 (0.21), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.85 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 482 
 HIS   0.001   0.000   HIS A 289 
 PHE   0.024   0.001   PHE B 555 
 TYR   0.008   0.001   TYR A 181 
 ARG   0.001   0.000   ARG B 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00323 (    2)
  link_NAG-ASN         : angle       1.83545 (    6)
  link_BETA1-4         : bond        0.00246 (    2)
  link_BETA1-4         : angle       4.33429 (    6)
  hydrogen bonds       : bond        0.04632 (  509)
  hydrogen bonds       : angle       4.01516 ( 1458)
  SS BOND              : bond        0.00141 (    8)
  SS BOND              : angle       0.73541 (   16)
  covalent geometry    : bond        0.00225 ( 8328)
  covalent geometry    : angle       0.97588 (11334)

*********************** 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
  117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 1.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  524 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.8183 (m-80)
REVERT: A  234 ASN cc_start: 0.8770 (t0) cc_final: 0.8491 (t0)
REVERT: A  524 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.7836 (m-80)
  outliers start: 13
  outliers final: 11
  residues processed: 114
  average time/residue: 0.3577
  time to fit residues: 59.8949
Evaluate side-chains
  117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  309 TYR
Chi-restraints excluded: chain B residue  347 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  524 TYR
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  524 TYR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  553 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 103 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0050
   chunk 105 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 101 optimal weight:    0.7980
   overall best weight:    1.5398

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

Flipped N/Q/H residues before XYZ refinement:
** A 235 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 = 0.3627 r_free = 0.3627 target = 0.118727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.097154 restraints weight = 40193.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.39
r_work: 0.3215 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8340  Z= 0.123
  Angle     :  0.980  36.529  11362  Z= 0.388
  Chirality :  0.038   0.204   1356
  Planarity :  0.005   0.067   1400
  Dihedral  :  5.695  54.698   1236
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.05 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.26), residues: 1076
  helix:  2.25 (0.21), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.89 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 482 
 HIS   0.002   0.001   HIS A 350 
 PHE   0.023   0.001   PHE A 555 
 TYR   0.009   0.001   TYR A 181 
 ARG   0.002   0.000   ARG A 103 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00346 (    2)
  link_NAG-ASN         : angle       2.15249 (    6)
  link_BETA1-4         : bond        0.00344 (    2)
  link_BETA1-4         : angle       4.28396 (    6)
  hydrogen bonds       : bond        0.04839 (  509)
  hydrogen bonds       : angle       4.03398 ( 1458)
  SS BOND              : bond        0.00178 (    8)
  SS BOND              : angle       0.89001 (   16)
  covalent geometry    : bond        0.00267 ( 8328)
  covalent geometry    : angle       0.97475 (11334)

********************** 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
  114 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  524 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8186 (m-80)
REVERT: A  524 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.7834 (m-80)
  outliers start: 13
  outliers final: 11
  residues processed: 111
  average time/residue: 0.3444
  time to fit residues: 57.0975
Evaluate side-chains
  113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  309 TYR
Chi-restraints excluded: chain B residue  347 ASP
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  524 TYR
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  553 LEU
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  524 TYR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  553 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0980
   chunk 89 optimal weight:    6.9990
   chunk 80 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   chunk 101 optimal weight:    0.7980
   chunk 1 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
** A 235 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 = 0.3657 r_free = 0.3657 target = 0.120329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.098359 restraints weight = 40589.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.52
r_work: 0.3234 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8340  Z= 0.099
  Angle     :  0.966  36.391  11362  Z= 0.377
  Chirality :  0.038   0.207   1356
  Planarity :  0.005   0.065   1400
  Dihedral  :  5.406  53.769   1236
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.05 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.27), residues: 1076
  helix:  2.44 (0.21), residues: 646
  sheet:  None (None), residues: 0
  loop : -0.72 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 482 
 HIS   0.001   0.000   HIS A 289 
 PHE   0.026   0.001   PHE B 555 
 TYR   0.007   0.001   TYR A 181 
 ARG   0.002   0.000   ARG A 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00347 (    2)
  link_NAG-ASN         : angle       2.13684 (    6)
  link_BETA1-4         : bond        0.00103 (    2)
  link_BETA1-4         : angle       3.49328 (    6)
  hydrogen bonds       : bond        0.04180 (  509)
  hydrogen bonds       : angle       3.87063 ( 1458)
  SS BOND              : bond        0.00122 (    8)
  SS BOND              : angle       0.58810 (   16)
  covalent geometry    : bond        0.00202 ( 8328)
  covalent geometry    : angle       0.96228 (11334)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7475.60 seconds
wall clock time: 128 minutes 39.12 seconds (7719.12 seconds total)