Starting phenix.real_space_refine
on Sun May 18 00:08:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8irp_35682/05_2025/8irp_35682_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8irp_35682/05_2025/8irp_35682.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8irp_35682/05_2025/8irp_35682.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8irp_35682/05_2025/8irp_35682.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8irp_35682/05_2025/8irp_35682_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8irp_35682/05_2025/8irp_35682_trim.cif"
  }
  resolution = 2.8
  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=   0.006
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    1474      1.98       5
     H    8208      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 16350
  Number of models: 1
  Model: ""
    Number of chains: 8
    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: {'H35': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 16
          Unusual residues: {'H35': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 8.30, per 1000 atoms: 0.51
  Number of scatterers: 16350
  At special positions: 0
  Unit cell: (94.461, 109.779, 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    1474      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=2.03
    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
    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: 5.07
  Conformation dependent library (CDL) restraints added in 1.5 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:
      54 helices and 6 sheets defined
      68.5% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  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: 4.233A  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: 3.855A  pdb=" N   ALA B 164 " --> pdb=" O   MET B 160 " (cutoff:3.500A)
      removed outlier: 3.907A  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 211
      removed outlier: 3.618A  pdb=" N   LEU B 207 " --> pdb=" O   PHE B 203 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL B 211 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 232
      removed outlier: 4.331A  pdb=" N   SER B 220 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
      removed outlier: 4.243A  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: 3.933A  pdb=" N   LYS B 355 " --> pdb=" O   ASP B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 375
      removed outlier: 3.668A  pdb=" N   ILE B 374 " --> pdb=" O   PHE B 371 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   ASN B 375 " --> pdb=" O   SER B 372 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 371 through 375'
    Processing helix  chain 'B' and resid 376 through 405
      removed outlier: 3.687A  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: 4.007A  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 495
      Proline residue:  B 486  - end of helix
    Processing helix  chain 'B' and resid 496 through 502
      removed outlier: 3.530A  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: 3.834A  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: 4.619A  pdb=" N   TRP B 543 " --> pdb=" O   VAL B 539 " (cutoff:3.500A)
      removed outlier: 5.105A  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 61
    Processing helix  chain 'A' and resid 62 through 73
      removed outlier: 4.233A  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: 3.855A  pdb=" N   ALA A 164 " --> pdb=" O   MET A 160 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   TYR A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 201
    Processing helix  chain 'A' and resid 203 through 211
      removed outlier: 3.618A  pdb=" N   LEU A 207 " --> pdb=" O   PHE A 203 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL A 211 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 232
      removed outlier: 4.332A  pdb=" N   SER A 220 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 4.242A  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: 3.933A  pdb=" N   LYS A 355 " --> pdb=" O   ASP A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 375
      removed outlier: 3.668A  pdb=" N   ILE A 374 " --> pdb=" O   PHE A 371 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   ASN A 375 " --> pdb=" O   SER A 372 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 371 through 375'
    Processing helix  chain 'A' and resid 376 through 405
      removed outlier: 3.687A  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 444 through 451
      removed outlier: 4.007A  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 495
      Proline residue:  A 486  - end of helix
    Processing helix  chain 'A' and resid 496 through 502
      removed outlier: 3.530A  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
      removed outlier: 3.833A  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: 4.619A  pdb=" N   TRP A 543 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
      removed outlier: 5.105A  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 274 through 275
      removed outlier: 3.685A  pdb=" N   SER B 274 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   SER B 261 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   SER A 261 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER A 274 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 286 through 287
      removed outlier: 3.819A  pdb=" N   SER B 261 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   SER A 261 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 87
    Processing sheet with id=AA6, first strand: chain 'A' and resid 156 through 158

    510 hydrogen bonds defined for protein.
    1446 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: 5.53

  Time building geometry restraints manager: 5.84 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: 3412
        1.42 -     1.62: 4824
        1.62 -     1.81: 84
  Bond restraints: 16538
  Sorted by residual:
  bond pdb=" C6  H35 A 701 "
       pdb=" N6  H35 A 701 "
    ideal  model  delta    sigma   weight residual
    1.345  1.447 -0.102 2.00e-02 2.50e+03 2.61e+01
  bond pdb=" C6  H35 B 701 "
       pdb=" N6  H35 B 701 "
    ideal  model  delta    sigma   weight residual
    1.345  1.447 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.465 -0.059 2.00e-02 2.50e+03 8.73e+00
  bond pdb=" CAM H35 B 701 "
       pdb=" CAO H35 B 701 "
    ideal  model  delta    sigma   weight residual
    1.429  1.386  0.043 2.00e-02 2.50e+03 4.67e+00
  bond pdb=" CAM H35 A 701 "
       pdb=" CAO H35 A 701 "
    ideal  model  delta    sigma   weight residual
    1.429  1.386  0.043 2.00e-02 2.50e+03 4.57e+00
  ... (remaining 16533 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 29627
        1.81 -     3.62: 251
        3.62 -     5.43: 38
        5.43 -     7.24: 4
        7.24 -     9.05: 6
  Bond angle restraints: 29926
  Sorted by residual:
  angle pdb=" N   LEU B 248 "
        pdb=" CA  LEU B 248 "
        pdb=" CB  LEU B 248 "
      ideal   model   delta    sigma   weight residual
     114.17  110.08    4.09 1.14e+00 7.69e-01 1.29e+01
  angle pdb=" N   LEU A 248 "
        pdb=" CA  LEU A 248 "
        pdb=" CB  LEU A 248 "
      ideal   model   delta    sigma   weight residual
     114.17  110.09    4.08 1.14e+00 7.69e-01 1.28e+01
  angle pdb=" C2  H35 A 701 "
        pdb=" N3  H35 A 701 "
        pdb=" C4  H35 A 701 "
      ideal   model   delta    sigma   weight residual
     113.07  122.12   -9.05 3.00e+00 1.11e-01 9.11e+00
  angle pdb=" C2  H35 B 701 "
        pdb=" N3  H35 B 701 "
        pdb=" C4  H35 B 701 "
      ideal   model   delta    sigma   weight residual
     113.07  122.11   -9.04 3.00e+00 1.11e-01 9.07e+00
  angle pdb=" CAP H35 A 701 "
        pdb=" CAK H35 A 701 "
        pdb=" OAL H35 A 701 "
      ideal   model   delta    sigma   weight residual
     118.02  126.33   -8.31 3.00e+00 1.11e-01 7.67e+00
  ... (remaining 29921 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.96: 7461
       24.96 -    49.93: 296
       49.93 -    74.89: 117
       74.89 -    99.86: 4
       99.86 -   124.82: 2
  Dihedral angle restraints: 7880
    sinusoidal: 4246
      harmonic: 3634
  Sorted by residual:
  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  143.50   36.50     0      5.00e+00 4.00e-02 5.33e+01
  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  143.56   36.44     0      5.00e+00 4.00e-02 5.31e+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 -159.40  -20.60     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 7877 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 1324
       0.099 -    0.199: 31
       0.199 -    0.298: 0
       0.298 -    0.398: 0
       0.398 -    0.497: 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   -1.90   -0.50 2.00e-01 2.50e+01 6.18e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 270 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.58    0.18 2.00e-01 2.50e+01 7.93e-01
  chirality pdb=" CA  ILE A 266 "
            pdb=" N   ILE A 266 "
            pdb=" C   ILE A 266 "
            pdb=" CB  ILE A 266 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.18e-01
  ... (remaining 1353 not shown)

  Planarity restraints: 2434
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 270 "   -0.094 2.00e-02 2.50e+03   7.85e-02 9.25e+01
        pdb=" CG  ASN B 270 "    0.020 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 270 "    0.044 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 270 "    0.085 2.00e-02 2.50e+03
        pdb="HD21 ASN B 270 "    0.065 2.00e-02 2.50e+03
        pdb=" C1  NAG D   1 "   -0.120 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 486 "   -0.039 5.00e-02 4.00e+02   5.81e-02 5.40e+00
        pdb=" N   PRO B 487 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B 487 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 487 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 486 "   -0.038 5.00e-02 4.00e+02   5.80e-02 5.38e+00
        pdb=" N   PRO A 487 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 487 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 487 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 2431 not shown)

  Histogram of nonbonded interaction distances:
        1.32 -     1.98: 122
        1.98 -     2.63: 21588
        2.63 -     3.29: 52563
        3.29 -     3.94: 67232
        3.94 -     4.60: 105585
  Nonbonded interactions: 247090
  Sorted by model distance:
  nonbonded pdb="HG23 THR A 162 "
            pdb=" HE1 PHE A 386 "
     model   vdw
     1.324 2.270
  nonbonded pdb="HG21 THR A 162 "
            pdb=" HD2 PRO A 438 "
     model   vdw
     1.376 2.440
  nonbonded pdb=" OD1 ASP A 130 "
            pdb=" HE2 HIS A 360 "
     model   vdw
     1.603 2.450
  nonbonded pdb=" OD1 ASP B 130 "
            pdb=" HE2 HIS B 360 "
     model   vdw
     1.603 2.450
  nonbonded pdb="HH22 ARG B 333 "
            pdb=" OD1 ASP B 347 "
     model   vdw
     1.606 2.450
  ... (remaining 247085 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  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:             0.290
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     36.930
  Find NCS groups from input model:        0.380
  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:12.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
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   0.102   8342  Z= 0.197
  Angle     :  0.645  12.829  11366  Z= 0.318
  Chirality :  0.042   0.497   1356
  Planarity :  0.004   0.058   1400
  Dihedral  : 13.359 124.823   2936
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.26), residues: 1076
  helix:  1.78 (0.20), residues: 654
  sheet: -5.81 (0.22), residues: 20
  loop : -0.48 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 482 
 HIS   0.001   0.000   HIS A 541 
 PHE   0.022   0.001   PHE A 203 
 TYR   0.010   0.001   TYR B 524 
 ARG   0.002   0.000   ARG A 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.07830 (    2)
  link_NAG-ASN         : angle       8.30898 (    6)
  link_BETA1-4         : bond        0.00442 (    2)
  link_BETA1-4         : angle       2.61143 (    6)
  hydrogen bonds       : bond        0.10724 (  506)
  hydrogen bonds       : angle       4.97067 ( 1446)
  SS BOND              : bond        0.00162 (    8)
  SS BOND              : angle       1.32796 (   16)
  covalent geometry    : bond        0.00387 ( 8330)
  covalent geometry    : angle       0.61162 (11338)

*********************** 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
  91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.168 
Fit side-chains
  outliers start: 0
  outliers final: 2
  residues processed: 91
  average time/residue: 2.2456
  time to fit residues: 219.9109
Evaluate side-chains
  80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  266 ILE
Chi-restraints excluded: chain A residue  266 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.3345 r_free = 0.3345 target = 0.118299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.097019 restraints weight = 28499.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 1.56
r_work: 0.2847 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.0758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8342  Z= 0.188
  Angle     :  0.570   7.923  11366  Z= 0.299
  Chirality :  0.041   0.139   1356
  Planarity :  0.004   0.057   1400
  Dihedral  :  8.100 108.033   1238
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  4.90 %
    Favored  : 94.41 %
  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:  1.07 (0.26), residues: 1076
  helix:  1.73 (0.20), residues: 648
  sheet: -5.71 (0.30), residues: 20
  loop : -0.59 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 380 
 HIS   0.002   0.001   HIS B 350 
 PHE   0.013   0.002   PHE A 166 
 TYR   0.010   0.002   TYR B 388 
 ARG   0.002   0.000   ARG A  42 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00262 (    2)
  link_NAG-ASN         : angle       2.01030 (    6)
  link_BETA1-4         : bond        0.00247 (    2)
  link_BETA1-4         : angle       3.11878 (    6)
  hydrogen bonds       : bond        0.04704 (  506)
  hydrogen bonds       : angle       4.49395 ( 1446)
  SS BOND              : bond        0.00175 (    8)
  SS BOND              : angle       1.59077 (   16)
  covalent geometry    : bond        0.00430 ( 8330)
  covalent geometry    : angle       0.56073 (11338)

*********************** 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
  84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 1.161 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 80
  average time/residue: 2.3358
  time to fit residues: 201.0582
Evaluate side-chains
  78 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  126 GLU
Chi-restraints excluded: chain A residue  126 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 88 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3244 r_free = 0.3244 target = 0.111720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.089502 restraints weight = 29282.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 1.67
r_work: 0.2846 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.0916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8342  Z= 0.133
  Angle     :  0.535   9.393  11366  Z= 0.276
  Chirality :  0.039   0.159   1356
  Planarity :  0.004   0.059   1400
  Dihedral  :  7.378  95.307   1234
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  6.76 %
    Favored  : 92.54 %
  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:  1.22 (0.26), residues: 1076
  helix:  1.83 (0.20), residues: 654
  sheet: -5.47 (0.42), residues: 20
  loop : -0.54 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 482 
 HIS   0.001   0.000   HIS B 541 
 PHE   0.014   0.001   PHE A 203 
 TYR   0.009   0.001   TYR B 388 
 ARG   0.001   0.000   ARG B 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00228 (    2)
  link_NAG-ASN         : angle       1.87237 (    6)
  link_BETA1-4         : bond        0.00459 (    2)
  link_BETA1-4         : angle       3.30873 (    6)
  hydrogen bonds       : bond        0.04217 (  506)
  hydrogen bonds       : angle       4.32365 ( 1446)
  SS BOND              : bond        0.00157 (    8)
  SS BOND              : angle       1.30818 (   16)
  covalent geometry    : bond        0.00295 ( 8330)
  covalent geometry    : angle       0.52577 (11338)

*********************** 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
  87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  494 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7184 (mpp)
REVERT: A  494 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7188 (mpp)
REVERT: A  509 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7561 (mt-10)
  outliers start: 6
  outliers final: 2
  residues processed: 81
  average time/residue: 2.2934
  time to fit residues: 199.5574
Evaluate side-chains
  82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  126 GLU
Chi-restraints excluded: chain B residue  494 MET
Chi-restraints excluded: chain A residue  126 GLU
Chi-restraints excluded: chain A residue  494 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3262 r_free = 0.3262 target = 0.112998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.090772 restraints weight = 29097.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 1.66
r_work: 0.2866 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.1090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8342  Z= 0.124
  Angle     :  0.527  10.891  11366  Z= 0.269
  Chirality :  0.039   0.130   1356
  Planarity :  0.004   0.059   1400
  Dihedral  :  6.606  77.829   1234
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  7.11 %
    Favored  : 91.96 %
  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:  1.30 (0.26), residues: 1076
  helix:  1.92 (0.20), residues: 654
  sheet: -5.37 (0.46), residues: 20
  loop : -0.56 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 482 
 HIS   0.001   0.000   HIS B 541 
 PHE   0.018   0.001   PHE B 203 
 TYR   0.009   0.001   TYR A 388 
 ARG   0.002   0.000   ARG B  23 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00154 (    2)
  link_NAG-ASN         : angle       1.94062 (    6)
  link_BETA1-4         : bond        0.00351 (    2)
  link_BETA1-4         : angle       3.58947 (    6)
  hydrogen bonds       : bond        0.03955 (  506)
  hydrogen bonds       : angle       4.20735 ( 1446)
  SS BOND              : bond        0.00185 (    8)
  SS BOND              : angle       1.26810 (   16)
  covalent geometry    : bond        0.00279 ( 8330)
  covalent geometry    : angle       0.51729 (11338)

*********************** 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
  88 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  494 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7165 (mpp)
REVERT: B  520 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8537 (mtt)
REVERT: A  494 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7167 (mpp)
REVERT: A  509 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7489 (mt-10)
  outliers start: 8
  outliers final: 1
  residues processed: 83
  average time/residue: 2.2338
  time to fit residues: 199.1978
Evaluate side-chains
  81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  494 MET
Chi-restraints excluded: chain B residue  520 MET
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  494 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0980
   chunk 7 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3260 r_free = 0.3260 target = 0.112963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.090627 restraints weight = 29428.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 1.68
r_work: 0.2862 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8342  Z= 0.117
  Angle     :  0.526  11.145  11366  Z= 0.267
  Chirality :  0.039   0.128   1356
  Planarity :  0.004   0.060   1400
  Dihedral  :  5.813  54.642   1234
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  8.16 %
    Favored  : 91.14 %
  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:  1.37 (0.26), residues: 1076
  helix:  2.01 (0.20), residues: 646
  sheet: -5.35 (0.47), residues: 20
  loop : -0.53 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 482 
 HIS   0.001   0.000   HIS B 541 
 PHE   0.018   0.001   PHE A 203 
 TYR   0.008   0.001   TYR B 388 
 ARG   0.003   0.000   ARG B  23 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00139 (    2)
  link_NAG-ASN         : angle       2.04295 (    6)
  link_BETA1-4         : bond        0.00072 (    2)
  link_BETA1-4         : angle       4.26200 (    6)
  hydrogen bonds       : bond        0.03914 (  506)
  hydrogen bonds       : angle       4.16044 ( 1446)
  SS BOND              : bond        0.00172 (    8)
  SS BOND              : angle       1.20458 (   16)
  covalent geometry    : bond        0.00259 ( 8330)
  covalent geometry    : angle       0.51380 (11338)

*********************** 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
  85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 1.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  494 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7187 (mpp)
REVERT: A  494 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7187 (mpp)
REVERT: A  509 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7476 (mt-10)
  outliers start: 6
  outliers final: 3
  residues processed: 81
  average time/residue: 2.2777
  time to fit residues: 198.6659
Evaluate side-chains
  82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  494 MET
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  494 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 59 optimal weight:    0.5980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3251 r_free = 0.3251 target = 0.112398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.090180 restraints weight = 29403.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 1.67
r_work: 0.2856 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8342  Z= 0.131
  Angle     :  0.525   8.531  11366  Z= 0.269
  Chirality :  0.039   0.134   1356
  Planarity :  0.004   0.059   1400
  Dihedral  :  5.118  47.686   1234
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  9.21 %
    Favored  : 90.21 %
  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:  1.37 (0.26), residues: 1076
  helix:  2.01 (0.20), residues: 646
  sheet: -5.25 (0.48), residues: 20
  loop : -0.53 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 482 
 HIS   0.001   0.000   HIS B 541 
 PHE   0.016   0.001   PHE A 203 
 TYR   0.009   0.001   TYR B 388 
 ARG   0.004   0.000   ARG A  23 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00115 (    2)
  link_NAG-ASN         : angle       2.33621 (    6)
  link_BETA1-4         : bond        0.00353 (    2)
  link_BETA1-4         : angle       4.82032 (    6)
  hydrogen bonds       : bond        0.03970 (  506)
  hydrogen bonds       : angle       4.14560 ( 1446)
  SS BOND              : bond        0.00178 (    8)
  SS BOND              : angle       1.28492 (   16)
  covalent geometry    : bond        0.00295 ( 8330)
  covalent geometry    : angle       0.50915 (11338)

*********************** 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
  81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 1.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  494 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7178 (mpp)
REVERT: A  494 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7190 (mpp)
REVERT: A  509 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7466 (mt-10)
  outliers start: 5
  outliers final: 3
  residues processed: 78
  average time/residue: 2.3990
  time to fit residues: 202.3037
Evaluate side-chains
  82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  494 MET
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  494 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3247 r_free = 0.3247 target = 0.112179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.090016 restraints weight = 29348.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 1.67
r_work: 0.2848 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8342  Z= 0.138
  Angle     :  0.521   7.995  11366  Z= 0.269
  Chirality :  0.039   0.147   1356
  Planarity :  0.004   0.060   1400
  Dihedral  :  5.020  46.893   1234
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.21 %
    Favored  : 90.09 %
  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:  1.35 (0.26), residues: 1076
  helix:  1.98 (0.20), residues: 646
  sheet: -5.28 (0.48), residues: 20
  loop : -0.53 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 482 
 HIS   0.001   0.000   HIS B 541 
 PHE   0.015   0.001   PHE A 203 
 TYR   0.009   0.001   TYR B 388 
 ARG   0.005   0.000   ARG A  23 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00182 (    2)
  link_NAG-ASN         : angle       2.45182 (    6)
  link_BETA1-4         : bond        0.00135 (    2)
  link_BETA1-4         : angle       4.48687 (    6)
  hydrogen bonds       : bond        0.03995 (  506)
  hydrogen bonds       : angle       4.15186 ( 1446)
  SS BOND              : bond        0.00173 (    8)
  SS BOND              : angle       1.32362 (   16)
  covalent geometry    : bond        0.00313 ( 8330)
  covalent geometry    : angle       0.50594 (11338)

*********************** 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
  84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  494 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7206 (mpp)
REVERT: A  494 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7218 (mpp)
REVERT: A  509 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7483 (mt-10)
  outliers start: 6
  outliers final: 3
  residues processed: 80
  average time/residue: 2.3617
  time to fit residues: 202.7694
Evaluate side-chains
  82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  494 MET
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  494 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3235 r_free = 0.3235 target = 0.111230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.089154 restraints weight = 29385.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 1.66
r_work: 0.2840 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8342  Z= 0.167
  Angle     :  0.536   7.460  11366  Z= 0.279
  Chirality :  0.040   0.155   1356
  Planarity :  0.005   0.060   1400
  Dihedral  :  5.100  46.158   1234
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  9.67 %
    Favored  : 89.74 %
  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:  1.26 (0.26), residues: 1076
  helix:  1.93 (0.20), residues: 644
  sheet: -5.24 (0.48), residues: 20
  loop : -0.59 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 482 
 HIS   0.002   0.001   HIS B 541 
 PHE   0.015   0.002   PHE B 203 
 TYR   0.009   0.001   TYR B 388 
 ARG   0.004   0.000   ARG A  23 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00113 (    2)
  link_NAG-ASN         : angle       2.34859 (    6)
  link_BETA1-4         : bond        0.00123 (    2)
  link_BETA1-4         : angle       4.28533 (    6)
  hydrogen bonds       : bond        0.04179 (  506)
  hydrogen bonds       : angle       4.19709 ( 1446)
  SS BOND              : bond        0.00197 (    8)
  SS BOND              : angle       1.48982 (   16)
  covalent geometry    : bond        0.00386 ( 8330)
  covalent geometry    : angle       0.52186 (11338)

*********************** 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
  82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  494 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7267 (mpp)
REVERT: A  494 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7279 (mpp)
REVERT: A  509 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7558 (mt-10)
  outliers start: 5
  outliers final: 3
  residues processed: 79
  average time/residue: 2.3812
  time to fit residues: 201.4968
Evaluate side-chains
  82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  494 MET
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  494 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 = 0.3274 r_free = 0.3274 target = 0.113457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.091944 restraints weight = 28956.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 1.59
r_work: 0.2827 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8342  Z= 0.177
  Angle     :  0.545   7.451  11366  Z= 0.284
  Chirality :  0.040   0.158   1356
  Planarity :  0.005   0.059   1400
  Dihedral  :  5.183  45.322   1234
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.81 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.02 %
    Favored  : 89.28 %
  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:  1.13 (0.25), residues: 1076
  helix:  1.83 (0.20), residues: 644
  sheet: -5.27 (0.48), residues: 20
  loop : -0.66 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 482 
 HIS   0.002   0.001   HIS B 541 
 PHE   0.016   0.002   PHE A 203 
 TYR   0.010   0.001   TYR B 388 
 ARG   0.004   0.000   ARG B  23 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00120 (    2)
  link_NAG-ASN         : angle       2.29903 (    6)
  link_BETA1-4         : bond        0.00098 (    2)
  link_BETA1-4         : angle       4.30861 (    6)
  hydrogen bonds       : bond        0.04268 (  506)
  hydrogen bonds       : angle       4.24276 ( 1446)
  SS BOND              : bond        0.00194 (    8)
  SS BOND              : angle       1.56185 (   16)
  covalent geometry    : bond        0.00410 ( 8330)
  covalent geometry    : angle       0.53066 (11338)

*********************** 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
  86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 1.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  494 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7313 (mpp)
REVERT: A  494 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7303 (mpp)
REVERT: A  509 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7602 (mt-10)
REVERT: A  520 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8444 (mtt)
  outliers start: 6
  outliers final: 3
  residues processed: 82
  average time/residue: 2.2847
  time to fit residues: 201.3090
Evaluate side-chains
  86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  494 MET
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  520 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    0.5980
   chunk 89 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
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 = 0.3227 r_free = 0.3227 target = 0.110645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.088647 restraints weight = 29350.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 1.65
r_work: 0.2830 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8342  Z= 0.174
  Angle     :  0.546   7.425  11366  Z= 0.284
  Chirality :  0.040   0.157   1356
  Planarity :  0.005   0.060   1400
  Dihedral  :  5.182  44.832   1234
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.90 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.14 %
    Favored  : 89.16 %
  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:  1.11 (0.25), residues: 1076
  helix:  1.82 (0.20), residues: 644
  sheet: -5.26 (0.49), residues: 20
  loop : -0.68 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 482 
 HIS   0.002   0.001   HIS B 541 
 PHE   0.016   0.002   PHE A 203 
 TYR   0.010   0.001   TYR B 388 
 ARG   0.004   0.000   ARG A  23 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00107 (    2)
  link_NAG-ASN         : angle       2.26056 (    6)
  link_BETA1-4         : bond        0.00090 (    2)
  link_BETA1-4         : angle       4.31756 (    6)
  hydrogen bonds       : bond        0.04263 (  506)
  hydrogen bonds       : angle       4.25410 ( 1446)
  SS BOND              : bond        0.00185 (    8)
  SS BOND              : angle       1.54057 (   16)
  covalent geometry    : bond        0.00405 ( 8330)
  covalent geometry    : angle       0.53230 (11338)

********************** 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
  86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 1.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  494 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7263 (mpp)
REVERT: A  494 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7280 (mpp)
REVERT: A  509 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7531 (mt-10)
REVERT: A  520 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8410 (mtt)
  outliers start: 6
  outliers final: 3
  residues processed: 82
  average time/residue: 2.3128
  time to fit residues: 203.4996
Evaluate side-chains
  86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 SER
Chi-restraints excluded: chain B residue  494 MET
Chi-restraints excluded: chain B residue  518 ILE
Chi-restraints excluded: chain A residue  220 SER
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain A residue  520 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 93 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0470
   chunk 8 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.0882

-------------------------------------------------------------------------------
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 = 0.3260 r_free = 0.3260 target = 0.112939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.091130 restraints weight = 29187.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 1.64
r_work: 0.2855 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8342  Z= 0.127
  Angle     :  0.518   7.137  11366  Z= 0.268
  Chirality :  0.039   0.150   1356
  Planarity :  0.004   0.060   1400
  Dihedral  :  5.008  44.254   1234
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.26 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.26), residues: 1076
  helix:  1.95 (0.20), residues: 646
  sheet: -5.32 (0.47), residues: 20
  loop : -0.60 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 482 
 HIS   0.001   0.000   HIS B 350 
 PHE   0.016   0.001   PHE A 203 
 TYR   0.009   0.001   TYR B 388 
 ARG   0.004   0.000   ARG B  23 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00179 (    2)
  link_NAG-ASN         : angle       2.16021 (    6)
  link_BETA1-4         : bond        0.00074 (    2)
  link_BETA1-4         : angle       4.14365 (    6)
  hydrogen bonds       : bond        0.03923 (  506)
  hydrogen bonds       : angle       4.17959 ( 1446)
  SS BOND              : bond        0.00167 (    8)
  SS BOND              : angle       1.26579 (   16)
  covalent geometry    : bond        0.00286 ( 8330)
  covalent geometry    : angle       0.50473 (11338)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8707.64 seconds
wall clock time: 149 minutes 42.99 seconds (8982.99 seconds total)