Starting phenix.real_space_refine
on Fri Jul  3 17:12:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jsj_22456/07_2026/7jsj_22456_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jsj_22456/07_2026/7jsj_22456.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jsj_22456/07_2026/7jsj_22456.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jsj_22456/07_2026/7jsj_22456.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jsj_22456/07_2026/7jsj_22456_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jsj_22456/07_2026/7jsj_22456_trim.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 16 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     Na      4      4.78       5
     C    4940      2.51       5
     N    1152      2.21       5
     O    1228      1.98       5
     H    7668      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 15056
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 7491
          Classifications: {'peptide': 468}
          Link IDs: {'PTRANS': 29, 'TRANS': 438}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 7491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 7491
          Classifications: {'peptide': 468}
          Link IDs: {'PTRANS': 29, 'TRANS': 438}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 35
          Ad-hoc single atom residues: {' NA': 2}
          Unusual residues: {'NAG': 1, 'X3M': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 35
          Ad-hoc single atom residues: {' NA': 2}
          Unusual residues: {'NAG': 1, 'X3M': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.16, per 1000 atoms: 0.14
  Number of scatterers: 15056
  At special positions: 0
  Unit cell: (85.84, 82.621, 108.373, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      64     16.00
     Na      4     11.00
     O    1228      8.00
     N    1152      7.00
     C    4940      6.00
     H    7668      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 562 "
      " NAG B 601 " - " ASN B 562 "
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 327.1 milliseconds
  

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1780

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      81.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 19
    Processing helix  chain 'A' and resid 20 through 29
      Proline residue:  A  26  - end of helix
      removed outlier: 3.695A  pdb=" N   ILE A  29 " --> pdb=" O   PRO A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 51
      removed outlier: 3.815A  pdb=" N   ARG A  37 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 61
    Processing helix  chain 'A' and resid 62 through 67
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 84 through 103
      removed outlier: 3.668A  pdb=" N   TRP A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 118
      removed outlier: 3.697A  pdb=" N   LEU A 111 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 137
      removed outlier: 3.543A  pdb=" N   LEU A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 158
      removed outlier: 3.809A  pdb=" N   THR A 144 " --> pdb=" O   SER A 140 " (cutoff:3.500A)
      Proline residue:  A 150  - end of helix
      removed outlier: 3.747A  pdb=" N   GLN A 158 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 220
      removed outlier: 3.993A  pdb=" N   LYS A 206 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   CYS A 213 " --> pdb=" O   THR A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 223
      No H-bonds generated for 'chain 'A' and resid 221 through 223'
    Processing helix  chain 'A' and resid 227 through 241
      removed outlier: 4.016A  pdb=" N   VAL A 231 " --> pdb=" O   THR A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 276
      Proline residue:  A 259  - end of helix
    Processing helix  chain 'A' and resid 292 through 297
    Processing helix  chain 'A' and resid 298 through 307
      removed outlier: 3.937A  pdb=" N   GLU A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 310
      No H-bonds generated for 'chain 'A' and resid 308 through 310'
    Processing helix  chain 'A' and resid 313 through 333
      removed outlier: 3.883A  pdb=" N   ILE A 317 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ASN A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ARG A 333 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 367
      removed outlier: 3.924A  pdb=" N   VAL A 359 " --> pdb=" O   SER A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 405
    Processing helix  chain 'A' and resid 408 through 428
      removed outlier: 3.580A  pdb=" N   LEU A 412 " --> pdb=" O   TRP A 408 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LEU A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLY A 415 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 436
    Processing helix  chain 'A' and resid 438 through 442
      removed outlier: 3.658A  pdb=" N   ALA A 442 " --> pdb=" O   PRO A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 460
    Processing helix  chain 'A' and resid 464 through 484
      removed outlier: 3.510A  pdb=" N   THR A 468 " --> pdb=" O   SER A 464 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   THR A 469 " --> pdb=" O   ASN A 465 " (cutoff:3.500A)
      Proline residue:  A 474  - end of helix
      removed outlier: 3.626A  pdb=" N   SER A 482 " --> pdb=" O   SER A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 498
      Proline residue:  A 493  - end of helix
    Processing helix  chain 'A' and resid 504 through 507
    Processing helix  chain 'A' and resid 508 through 516
      removed outlier: 3.659A  pdb=" N   ALA A 512 " --> pdb=" O   THR A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 547
      removed outlier: 3.671A  pdb=" N   MET A 525 " --> pdb=" O   LYS A 521 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   ILE A 531 " --> pdb=" O   LYS A 527 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   MET A 532 " --> pdb=" O   THR A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 553
      removed outlier: 4.084A  pdb=" N   ILE A 551 " --> pdb=" O   TRP A 547 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   PHE A 552 " --> pdb=" O   GLY A 548 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 19
    Processing helix  chain 'B' and resid 20 through 29
      Proline residue:  B  26  - end of helix
      removed outlier: 3.695A  pdb=" N   ILE B  29 " --> pdb=" O   PRO B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 51
      removed outlier: 3.816A  pdb=" N   ARG B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 61
    Processing helix  chain 'B' and resid 62 through 67
    Processing helix  chain 'B' and resid 75 through 80
    Processing helix  chain 'B' and resid 84 through 103
      removed outlier: 3.667A  pdb=" N   TRP B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 118
      removed outlier: 3.698A  pdb=" N   LEU B 111 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU B 115 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 137
      removed outlier: 3.544A  pdb=" N   LEU B 126 " --> pdb=" O   ALA B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 158
      removed outlier: 3.809A  pdb=" N   THR B 144 " --> pdb=" O   SER B 140 " (cutoff:3.500A)
      Proline residue:  B 150  - end of helix
      removed outlier: 3.748A  pdb=" N   GLN B 158 " --> pdb=" O   ALA B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 220
      removed outlier: 3.992A  pdb=" N   LYS B 206 " --> pdb=" O   LYS B 202 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   CYS B 213 " --> pdb=" O   THR B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 223
      No H-bonds generated for 'chain 'B' and resid 221 through 223'
    Processing helix  chain 'B' and resid 227 through 241
      removed outlier: 4.015A  pdb=" N   VAL B 231 " --> pdb=" O   THR B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 276
      Proline residue:  B 259  - end of helix
    Processing helix  chain 'B' and resid 292 through 297
    Processing helix  chain 'B' and resid 298 through 307
      removed outlier: 3.937A  pdb=" N   GLU B 304 " --> pdb=" O   LYS B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 310
      No H-bonds generated for 'chain 'B' and resid 308 through 310'
    Processing helix  chain 'B' and resid 313 through 333
      removed outlier: 3.883A  pdb=" N   ILE B 317 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ASN B 318 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ARG B 333 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 367
      removed outlier: 3.923A  pdb=" N   VAL B 359 " --> pdb=" O   SER B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 405
    Processing helix  chain 'B' and resid 408 through 428
      removed outlier: 3.581A  pdb=" N   LEU B 412 " --> pdb=" O   TRP B 408 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU B 414 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLY B 415 " --> pdb=" O   VAL B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 436
    Processing helix  chain 'B' and resid 438 through 442
      removed outlier: 3.658A  pdb=" N   ALA B 442 " --> pdb=" O   PRO B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 460
    Processing helix  chain 'B' and resid 464 through 484
      removed outlier: 3.509A  pdb=" N   THR B 468 " --> pdb=" O   SER B 464 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   THR B 469 " --> pdb=" O   ASN B 465 " (cutoff:3.500A)
      Proline residue:  B 474  - end of helix
      removed outlier: 3.625A  pdb=" N   SER B 482 " --> pdb=" O   SER B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 498
      Proline residue:  B 493  - end of helix
    Processing helix  chain 'B' and resid 504 through 507
    Processing helix  chain 'B' and resid 508 through 516
      removed outlier: 3.659A  pdb=" N   ALA B 512 " --> pdb=" O   THR B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 547
      removed outlier: 3.671A  pdb=" N   MET B 525 " --> pdb=" O   LYS B 521 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ILE B 531 " --> pdb=" O   LYS B 527 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   MET B 532 " --> pdb=" O   THR B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 553
      removed outlier: 4.085A  pdb=" N   ILE B 551 " --> pdb=" O   TRP B 547 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   PHE B 552 " --> pdb=" O   GLY B 548 " (cutoff:3.500A)

    446 hydrogen bonds defined for protein.
    1296 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.93

  Time building geometry restraints manager: 1.55 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: 7648
        1.03 -     1.22: 22
        1.22 -     1.42: 3016
        1.42 -     1.61: 4450
        1.61 -     1.81: 108
  Bond restraints: 15244
  Sorted by residual:
  bond pdb=" C1  NAG B 601 "
       pdb=" C2  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.532  1.599 -0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" C1  NAG A 601 "
       pdb=" C2  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.532  1.598 -0.066 2.00e-02 2.50e+03 1.10e+01
  bond pdb=" C7  NAG A 601 "
       pdb=" N2  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.346  1.393 -0.047 2.00e-02 2.50e+03 5.50e+00
  bond pdb=" C7  NAG B 601 "
       pdb=" N2  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.346  1.393 -0.047 2.00e-02 2.50e+03 5.43e+00
  bond pdb=" C02 X3M A 602 "
       pdb=" C05 X3M A 602 "
    ideal  model  delta    sigma   weight residual
    1.526  1.487  0.039 2.00e-02 2.50e+03 3.84e+00
  ... (remaining 15239 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.26: 27500
        7.26 -    14.52: 32
       14.52 -    21.79: 22
       21.79 -    29.05: 136
       29.05 -    36.31: 58
  Bond angle restraints: 27748
  Sorted by residual:
  angle pdb=" CB  VAL A 263 "
        pdb=" CA  VAL A 263 "
        pdb=" HA  VAL A 263 "
      ideal   model   delta    sigma   weight residual
     109.00   72.69   36.31 3.00e+00 1.11e-01 1.46e+02
  angle pdb=" CB  VAL B 263 "
        pdb=" CA  VAL B 263 "
        pdb=" HA  VAL B 263 "
      ideal   model   delta    sigma   weight residual
     109.00   72.86   36.14 3.00e+00 1.11e-01 1.45e+02
  angle pdb=" C   SER B 291 "
        pdb=" CA  SER B 291 "
        pdb=" HA  SER B 291 "
      ideal   model   delta    sigma   weight residual
     109.00   73.34   35.66 3.00e+00 1.11e-01 1.41e+02
  angle pdb=" C   SER A 291 "
        pdb=" CA  SER A 291 "
        pdb=" HA  SER A 291 "
      ideal   model   delta    sigma   weight residual
     109.00   73.62   35.38 3.00e+00 1.11e-01 1.39e+02
  angle pdb=" N   SER A 291 "
        pdb=" CA  SER A 291 "
        pdb=" HA  SER A 291 "
      ideal   model   delta    sigma   weight residual
     110.00   74.85   35.15 3.00e+00 1.11e-01 1.37e+02
  ... (remaining 27743 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.55: 6452
       16.55 -    33.10: 491
       33.10 -    49.65: 167
       49.65 -    66.21: 83
       66.21 -    82.76: 9
  Dihedral angle restraints: 7202
    sinusoidal: 3898
      harmonic: 3304
  Sorted by residual:
  dihedral pdb=" CA  THR B 225 "
           pdb=" C   THR B 225 "
           pdb=" N   GLY B 226 "
           pdb=" CA  GLY B 226 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.59   27.41     0      5.00e+00 4.00e-02 3.01e+01
  dihedral pdb=" CA  THR A 225 "
           pdb=" C   THR A 225 "
           pdb=" N   GLY A 226 "
           pdb=" CA  GLY A 226 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.60   27.40     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CA  TYR A 353 "
           pdb=" C   TYR A 353 "
           pdb=" N   VAL A 354 "
           pdb=" CA  VAL A 354 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.73  -25.27     0      5.00e+00 4.00e-02 2.55e+01
  ... (remaining 7199 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.345: 1232
       0.345 -    0.689: 2
       0.689 -    1.034: 0
       1.034 -    1.378: 4
       1.378 -    1.723: 12
  Chirality restraints: 1250
  Sorted by residual:
  chirality pdb=" CG  LEU B  27 "
            pdb=" CB  LEU B  27 "
            pdb=" CD1 LEU B  27 "
            pdb=" CD2 LEU B  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.87   -1.72 2.00e-01 2.50e+01 7.42e+01
  chirality pdb=" CG  LEU A  27 "
            pdb=" CB  LEU A  27 "
            pdb=" CD1 LEU A  27 "
            pdb=" CD2 LEU A  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.87   -1.72 2.00e-01 2.50e+01 7.36e+01
  chirality pdb=" CG  LEU A  23 "
            pdb=" CB  LEU A  23 "
            pdb=" CD1 LEU A  23 "
            pdb=" CD2 LEU A  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.90   -1.69 2.00e-01 2.50e+01 7.10e+01
  ... (remaining 1247 not shown)

  Planarity restraints: 2106
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 406 "   -0.031 5.00e-02 4.00e+02   4.60e-02 3.39e+00
        pdb=" N   PRO B 407 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 407 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 407 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 406 "   -0.030 5.00e-02 4.00e+02   4.58e-02 3.36e+00
        pdb=" N   PRO A 407 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 407 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 407 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 310 "   -0.029 5.00e-02 4.00e+02   4.45e-02 3.16e+00
        pdb=" N   PRO A 311 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 311 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 311 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 2103 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 841
        2.16 -     2.77: 29736
        2.77 -     3.38: 41996
        3.38 -     3.99: 53957
        3.99 -     4.60: 88078
  Nonbonded interactions: 214608
  Sorted by model distance:
  nonbonded pdb=" O   THR B 225 "
            pdb=" H   THR B 227 "
     model   vdw
     1.553 2.450
  nonbonded pdb=" O   THR A 225 "
            pdb=" H   THR A 227 "
     model   vdw
     1.554 2.450
  nonbonded pdb=" O   MET A  31 "
            pdb=" H   ALA A  33 "
     model   vdw
     1.558 2.450
  nonbonded pdb=" O   MET B  31 "
            pdb=" H   ALA B  33 "
     model   vdw
     1.558 2.450
  nonbonded pdb=" HA  VAL A 263 "
            pdb=" HB  VAL A 263 "
     model   vdw
     1.587 1.952
  ... (remaining 214603 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.090
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.770
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
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      :  0.008   0.067   7578  Z= 0.304
  Angle     :  1.100  26.291  10342  Z= 0.483
  Chirality :  0.182   1.723   1250
  Planarity :  0.005   0.046   1236
  Dihedral  : 12.914  65.085   2722
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  9.17 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  7.23 %
    Allowed  :  8.73 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.30), residues: 916
  helix:  0.84 (0.21), residues: 682
  sheet:  None (None), residues: 0
  loop : -3.23 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 102 
 TYR   0.012   0.001   TYR A 353 
 PHE   0.019   0.001   PHE A  35 
 TRP   0.010   0.002   TRP A 560 
 HIS   0.002   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00790 /  0.30 ( 7576)
  covalent geometry    : angle       1.09795 /  0.48 (10336)
  hydrogen bonds       : bond        0.14111 /  9.65 (  446)
  hydrogen bonds       : angle       5.71546 /  4.02 ( 1296)
  link_NAG-ASN         : bond        0.00865 /  0.43 (    2)
  link_NAG-ASN         : angle       2.90525 /  1.32 (    6)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 102
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6705 (mmt)
REVERT: A  240 LEU cc_start: 0.8040 (mt) cc_final: 0.7617 (mt)
REVERT: A  312 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6461 (tt)
REVERT: A  391 PHE cc_start: 0.4442 (OUTLIER) cc_final: 0.3827 (m-80)
REVERT: A  392 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.5332 (m-80)
REVERT: A  458 VAL cc_start: 0.8314 (t) cc_final: 0.8111 (m)
REVERT: B  115 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7978 (mt)
REVERT: B  158 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6322 (mm-40)
REVERT: B  312 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7166 (tt)
REVERT: B  369 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7897 (pt)
REVERT: B  391 PHE cc_start: 0.4144 (OUTLIER) cc_final: 0.3228 (t80)
REVERT: B  392 TYR cc_start: 0.3641 (OUTLIER) cc_final: 0.2582 (m-80)
  outliers start: 58
  outliers final: 18
  residues processed: 154
  average time/residue: 0.1576
  time to fit residues: 33.5532
Evaluate side-chains
  109 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 81
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   31 MET
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue   88 MET
Chi-restraints excluded: chain A residue  106 HIS
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  376 LYS
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue  106 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  138 TRP
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain B residue  391 PHE
Chi-restraints excluded: chain B residue  392 TYR
Chi-restraints excluded: chain B residue  519 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0980
   chunk 51 optimal weight:    0.0870
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.3158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 545 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.149344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.136320 restraints weight = 22825.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 1.56
r_work: 0.3621 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3500 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7578  Z= 0.149
  Angle     :  1.075  26.412  10342  Z= 0.478
  Chirality :  0.181   1.735   1250
  Planarity :  0.006   0.056   1236
  Dihedral  :  9.430  88.444   1105
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.53 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 11.35 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.30), residues: 916
  helix:  1.10 (0.21), residues: 688
  sheet:  None (None), residues: 0
  loop : -3.25 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 108 
 TYR   0.009   0.001   TYR B 353 
 PHE   0.017   0.001   PHE B 258 
 TRP   0.009   0.001   TRP B  49 
 HIS   0.006   0.001   HIS A 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 ( 7576)
  covalent geometry    : angle       1.07350 /  0.48 (10336)
  hydrogen bonds       : bond        0.04944 /  3.17 (  446)
  hydrogen bonds       : angle       4.51143 /  3.18 ( 1296)
  link_NAG-ASN         : bond        0.00784 /  0.39 (    2)
  link_NAG-ASN         : angle       2.56216 /  1.16 (    6)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 83
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6254 (tt)
REVERT: A  376 LYS cc_start: 0.2987 (OUTLIER) cc_final: 0.2771 (mmtt)
REVERT: A  391 PHE cc_start: 0.4639 (OUTLIER) cc_final: 0.4032 (m-80)
REVERT: A  392 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.5418 (m-80)
REVERT: B  115 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7792 (mt)
REVERT: B  158 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6644 (mm-40)
REVERT: B  202 LYS cc_start: 0.6935 (mtmt) cc_final: 0.6676 (tptt)
REVERT: B  312 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7212 (tt)
REVERT: B  391 PHE cc_start: 0.3679 (OUTLIER) cc_final: 0.2679 (t80)
REVERT: B  392 TYR cc_start: 0.3680 (OUTLIER) cc_final: 0.2700 (m-80)
REVERT: B  413 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7289 (tt)
  outliers start: 34
  outliers final: 21
  residues processed: 112
  average time/residue: 0.1330
  time to fit residues: 22.0342
Evaluate side-chains
  108 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   31 MET
Chi-restraints excluded: chain A residue  106 HIS
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  376 LYS
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  545 ASN
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  106 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  138 TRP
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  249 ASN
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  391 PHE
Chi-restraints excluded: chain B residue  392 TYR
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  519 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 86 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 104 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.146350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.133171 restraints weight = 23232.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 1.60
r_work: 0.3550 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7578  Z= 0.164
  Angle     :  1.060  26.301  10342  Z= 0.469
  Chirality :  0.182   1.719   1250
  Planarity :  0.006   0.055   1236
  Dihedral  :  9.056  87.129   1096
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 11.97 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.30), residues: 916
  helix:  1.41 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.73 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 108 
 TYR   0.010   0.001   TYR B 353 
 PHE   0.015   0.001   PHE B 258 
 TRP   0.011   0.001   TRP A  49 
 HIS   0.006   0.001   HIS A 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.16 ( 7576)
  covalent geometry    : angle       1.05814 /  0.47 (10336)
  hydrogen bonds       : bond        0.04978 /  3.21 (  446)
  hydrogen bonds       : angle       4.33634 /  3.05 ( 1296)
  link_NAG-ASN         : bond        0.00759 /  0.38 (    2)
  link_NAG-ASN         : angle       2.78094 /  1.26 (    6)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 105
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  277 MET cc_start: 0.7604 (mtt) cc_final: 0.7371 (mtp)
REVERT: A  312 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6286 (tt)
REVERT: A  376 LYS cc_start: 0.2989 (OUTLIER) cc_final: 0.2673 (mmmt)
REVERT: A  391 PHE cc_start: 0.4733 (OUTLIER) cc_final: 0.4068 (m-80)
REVERT: A  392 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.5511 (m-80)
REVERT: A  556 HIS cc_start: 0.7445 (m-70) cc_final: 0.7019 (m90)
REVERT: B  115 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7853 (mt)
REVERT: B  158 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6643 (mm-40)
REVERT: B  312 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7348 (tt)
REVERT: B  369 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7964 (pt)
REVERT: B  391 PHE cc_start: 0.3789 (OUTLIER) cc_final: 0.2680 (t80)
REVERT: B  392 TYR cc_start: 0.3738 (OUTLIER) cc_final: 0.2886 (m-80)
REVERT: B  413 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7391 (tt)
REVERT: B  517 TYR cc_start: 0.8694 (m-80) cc_final: 0.8430 (m-80)
  outliers start: 38
  outliers final: 23
  residues processed: 135
  average time/residue: 0.1216
  time to fit residues: 24.5349
Evaluate side-chains
  130 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 96
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   31 MET
Chi-restraints excluded: chain A residue  106 HIS
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  376 LYS
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   60 SER
Chi-restraints excluded: chain B residue  106 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  138 TRP
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  249 ASN
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain B residue  391 PHE
Chi-restraints excluded: chain B residue  392 TYR
Chi-restraints excluded: chain B residue  402 THR
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  519 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0980
   chunk 86 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0980
   chunk 71 optimal weight:    0.0970
   overall best weight:    0.3578

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.147168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.133910 restraints weight = 23208.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 1.62
r_work: 0.3553 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3429 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7578  Z= 0.132
  Angle     :  1.037  26.144  10342  Z= 0.453
  Chirality :  0.182   1.734   1250
  Planarity :  0.006   0.057   1236
  Dihedral  :  8.738  83.090   1094
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 11.85 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.30), residues: 916
  helix:  1.52 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.70 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 108 
 TYR   0.011   0.001   TYR A 517 
 PHE   0.011   0.001   PHE A  35 
 TRP   0.010   0.001   TRP A  49 
 HIS   0.007   0.001   HIS A 556 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.13 ( 7576)
  covalent geometry    : angle       1.03550 /  0.45 (10336)
  hydrogen bonds       : bond        0.04205 /  2.68 (  446)
  hydrogen bonds       : angle       4.10186 /  2.90 ( 1296)
  link_NAG-ASN         : bond        0.00868 /  0.44 (    2)
  link_NAG-ASN         : angle       2.72702 /  1.24 (    6)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 101
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LEU cc_start: 0.7298 (mm) cc_final: 0.7095 (mt)
REVERT: A  201 ARG cc_start: 0.6445 (mmm160) cc_final: 0.5965 (mmm160)
REVERT: A  277 MET cc_start: 0.7695 (mtt) cc_final: 0.7476 (mtp)
REVERT: A  312 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6306 (tt)
REVERT: A  376 LYS cc_start: 0.2934 (OUTLIER) cc_final: 0.2657 (mmmt)
REVERT: A  391 PHE cc_start: 0.4753 (OUTLIER) cc_final: 0.3992 (m-80)
REVERT: A  392 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.5409 (m-80)
REVERT: B  115 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7778 (mt)
REVERT: B  158 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6555 (mm-40)
REVERT: B  312 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7301 (tt)
REVERT: B  369 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7951 (pt)
REVERT: B  391 PHE cc_start: 0.3983 (OUTLIER) cc_final: 0.2771 (t80)
REVERT: B  392 TYR cc_start: 0.3974 (OUTLIER) cc_final: 0.3134 (m-80)
REVERT: B  413 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7369 (tt)
REVERT: B  517 TYR cc_start: 0.8612 (m-80) cc_final: 0.8342 (m-80)
  outliers start: 39
  outliers final: 25
  residues processed: 131
  average time/residue: 0.1419
  time to fit residues: 26.9926
Evaluate side-chains
  132 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 96
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   31 MET
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  376 LYS
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   60 SER
Chi-restraints excluded: chain B residue  106 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  138 TRP
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  249 ASN
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain B residue  391 PHE
Chi-restraints excluded: chain B residue  392 TYR
Chi-restraints excluded: chain B residue  402 THR
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  494 CYS
Chi-restraints excluded: chain B residue  519 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 83 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 545 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.139248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.125780 restraints weight = 23872.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 1.65
r_work: 0.3486 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7578  Z= 0.172
  Angle     :  1.050  26.229  10342  Z= 0.462
  Chirality :  0.183   1.725   1250
  Planarity :  0.006   0.056   1236
  Dihedral  :  8.705  80.412   1092
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 12.97 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.30), residues: 916
  helix:  1.49 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.66 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 108 
 TYR   0.010   0.001   TYR B 353 
 PHE   0.014   0.001   PHE A  35 
 TRP   0.010   0.001   TRP A  49 
 HIS   0.007   0.002   HIS A 556 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00415 /  0.17 ( 7576)
  covalent geometry    : angle       1.04777 /  0.46 (10336)
  hydrogen bonds       : bond        0.04728 /  3.01 (  446)
  hydrogen bonds       : angle       4.13164 /  2.92 ( 1296)
  link_NAG-ASN         : bond        0.00849 /  0.42 (    2)
  link_NAG-ASN         : angle       2.76745 /  1.26 (    6)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 106
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 ARG cc_start: 0.6720 (mmm160) cc_final: 0.6188 (mmm160)
REVERT: A  277 MET cc_start: 0.7562 (mtt) cc_final: 0.7336 (mtp)
REVERT: A  312 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6394 (tt)
REVERT: A  376 LYS cc_start: 0.3098 (OUTLIER) cc_final: 0.2818 (mmtt)
REVERT: A  391 PHE cc_start: 0.4823 (OUTLIER) cc_final: 0.3997 (m-80)
REVERT: A  392 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.5437 (m-80)
REVERT: B  115 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7891 (mt)
REVERT: B  312 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7394 (tt)
REVERT: B  324 PHE cc_start: 0.8322 (m-80) cc_final: 0.8070 (m-10)
REVERT: B  391 PHE cc_start: 0.3964 (OUTLIER) cc_final: 0.2764 (t80)
REVERT: B  392 TYR cc_start: 0.3577 (OUTLIER) cc_final: 0.2762 (m-80)
REVERT: B  410 ILE cc_start: 0.8642 (tt) cc_final: 0.8420 (tp)
REVERT: B  413 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7564 (tt)
REVERT: B  517 TYR cc_start: 0.8542 (m-80) cc_final: 0.8298 (m-80)
  outliers start: 36
  outliers final: 25
  residues processed: 133
  average time/residue: 0.1293
  time to fit residues: 25.6209
Evaluate side-chains
  137 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   31 MET
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  376 LYS
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   60 SER
Chi-restraints excluded: chain B residue  106 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  138 TRP
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  249 ASN
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain B residue  391 PHE
Chi-restraints excluded: chain B residue  392 TYR
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  402 THR
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  494 CYS
Chi-restraints excluded: chain B residue  519 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0970
   chunk 87 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 80 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 238 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.144049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.130407 restraints weight = 23472.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 1.67
r_work: 0.3514 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3387 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7578  Z= 0.134
  Angle     :  1.031  26.146  10342  Z= 0.449
  Chirality :  0.182   1.732   1250
  Planarity :  0.005   0.051   1236
  Dihedral  :  8.385  79.691   1089
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 13.84 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.30), residues: 916
  helix:  1.62 (0.21), residues: 662
  sheet:  None (None), residues: 0
  loop : -2.50 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 102 
 TYR   0.010   0.001   TYR B 214 
 PHE   0.011   0.001   PHE B  35 
 TRP   0.010   0.001   TRP A  49 
 HIS   0.009   0.002   HIS A 556 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.13 ( 7576)
  covalent geometry    : angle       1.02926 /  0.45 (10336)
  hydrogen bonds       : bond        0.04142 /  2.64 (  446)
  hydrogen bonds       : angle       4.00382 /  2.83 ( 1296)
  link_NAG-ASN         : bond        0.00858 /  0.43 (    2)
  link_NAG-ASN         : angle       2.76732 /  1.26 (    6)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 103
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 ARG cc_start: 0.6685 (mmm160) cc_final: 0.6137 (mmm160)
REVERT: A  277 MET cc_start: 0.7631 (mtt) cc_final: 0.7399 (mtp)
REVERT: A  312 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6268 (tt)
REVERT: A  376 LYS cc_start: 0.3094 (OUTLIER) cc_final: 0.2818 (mmtt)
REVERT: A  391 PHE cc_start: 0.4798 (OUTLIER) cc_final: 0.3900 (m-80)
REVERT: A  392 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.5405 (m-10)
REVERT: B  115 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7995 (mt)
REVERT: B  312 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7372 (tt)
REVERT: B  391 PHE cc_start: 0.3938 (OUTLIER) cc_final: 0.2801 (t80)
REVERT: B  392 TYR cc_start: 0.3622 (OUTLIER) cc_final: 0.2817 (m-80)
REVERT: B  410 ILE cc_start: 0.8587 (tt) cc_final: 0.8373 (tp)
REVERT: B  413 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7533 (tt)
  outliers start: 34
  outliers final: 24
  residues processed: 129
  average time/residue: 0.1410
  time to fit residues: 26.6237
Evaluate side-chains
  132 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 99
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   31 MET
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  376 LYS
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  106 HIS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  138 TRP
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  249 ASN
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  369 ILE
Chi-restraints excluded: chain B residue  391 PHE
Chi-restraints excluded: chain B residue  392 TYR
Chi-restraints excluded: chain B residue  402 THR
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  494 CYS
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain B residue  559 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 13 optimal weight:    0.4980
   chunk 40 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 30 optimal weight:    0.1980
   chunk 83 optimal weight:    0.0870
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.4158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 238 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.143726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.130051 restraints weight = 23541.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 1.67
r_work: 0.3511 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3390 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7578  Z= 0.132
  Angle     :  1.026  26.212  10342  Z= 0.445
  Chirality :  0.182   1.728   1250
  Planarity :  0.005   0.051   1236
  Dihedral  :  8.242  79.707   1087
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 13.09 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.30), residues: 916
  helix:  1.69 (0.21), residues: 662
  sheet:  None (None), residues: 0
  loop : -2.45 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 108 
 TYR   0.009   0.001   TYR B 353 
 PHE   0.012   0.001   PHE A  35 
 TRP   0.011   0.001   TRP B  49 
 HIS   0.006   0.002   HIS A 556 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.13 ( 7576)
  covalent geometry    : angle       1.02404 /  0.44 (10336)
  hydrogen bonds       : bond        0.04057 /  2.58 (  446)
  hydrogen bonds       : angle       3.93979 /  2.78 ( 1296)
  link_NAG-ASN         : bond        0.00885 /  0.44 (    2)
  link_NAG-ASN         : angle       2.72032 /  1.23 (    6)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 ARG cc_start: 0.6742 (mmm160) cc_final: 0.6215 (mmm160)
REVERT: A  277 MET cc_start: 0.7530 (mtt) cc_final: 0.7305 (mtp)
REVERT: A  304 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6298 (mp0)
REVERT: A  312 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6182 (tt)
REVERT: A  376 LYS cc_start: 0.3061 (OUTLIER) cc_final: 0.2758 (mmtt)
REVERT: A  391 PHE cc_start: 0.4820 (OUTLIER) cc_final: 0.3851 (m-80)
REVERT: A  392 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.5373 (m-80)
REVERT: B  312 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7428 (tt)
REVERT: B  391 PHE cc_start: 0.4145 (OUTLIER) cc_final: 0.2924 (t80)
REVERT: B  392 TYR cc_start: 0.4017 (OUTLIER) cc_final: 0.3227 (m-80)
REVERT: B  410 ILE cc_start: 0.8588 (tt) cc_final: 0.8381 (tp)
REVERT: B  413 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7558 (tt)
  outliers start: 36
  outliers final: 25
  residues processed: 131
  average time/residue: 0.1362
  time to fit residues: 26.0678
Evaluate side-chains
  135 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 101
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   31 MET
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  376 LYS
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  528 THR
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   60 SER
Chi-restraints excluded: chain B residue  106 HIS
Chi-restraints excluded: chain B residue  138 TRP
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  249 ASN
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  391 PHE
Chi-restraints excluded: chain B residue  392 TYR
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  402 THR
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  494 CYS
Chi-restraints excluded: chain B residue  519 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 50 optimal weight:    0.3980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 238 ASN
A 545 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.137947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.124147 restraints weight = 24100.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 1.69
r_work: 0.3462 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7578  Z= 0.163
  Angle     :  1.039  26.168  10342  Z= 0.456
  Chirality :  0.182   1.727   1250
  Planarity :  0.005   0.047   1236
  Dihedral  :  8.137  77.547   1085
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 13.47 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.30), residues: 916
  helix:  1.54 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.49 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 108 
 TYR   0.009   0.001   TYR B 353 
 PHE   0.015   0.001   PHE B  35 
 TRP   0.011   0.001   TRP A  49 
 HIS   0.006   0.002   HIS A 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.16 ( 7576)
  covalent geometry    : angle       1.03725 /  0.46 (10336)
  hydrogen bonds       : bond        0.04526 /  2.88 (  446)
  hydrogen bonds       : angle       4.00572 /  2.85 ( 1296)
  link_NAG-ASN         : bond        0.00866 /  0.43 (    2)
  link_NAG-ASN         : angle       2.75247 /  1.24 (    6)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 ARG cc_start: 0.6930 (mmm160) cc_final: 0.6383 (mmm160)
REVERT: A  208 MET cc_start: 0.7171 (mmm) cc_final: 0.6939 (mmt)
REVERT: A  277 MET cc_start: 0.7655 (mtt) cc_final: 0.7428 (mtp)
REVERT: A  304 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6390 (mp0)
REVERT: A  312 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6300 (tt)
REVERT: A  376 LYS cc_start: 0.3138 (OUTLIER) cc_final: 0.2741 (mmtt)
REVERT: A  391 PHE cc_start: 0.4819 (OUTLIER) cc_final: 0.3784 (m-80)
REVERT: A  392 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.5402 (m-80)
REVERT: B  312 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7435 (tt)
REVERT: B  391 PHE cc_start: 0.4120 (OUTLIER) cc_final: 0.3051 (t80)
REVERT: B  392 TYR cc_start: 0.3764 (OUTLIER) cc_final: 0.2902 (m-80)
REVERT: B  413 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7668 (tt)
  outliers start: 33
  outliers final: 22
  residues processed: 130
  average time/residue: 0.1326
  time to fit residues: 25.8172
Evaluate side-chains
  130 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 99
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   31 MET
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  376 LYS
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   60 SER
Chi-restraints excluded: chain B residue  106 HIS
Chi-restraints excluded: chain B residue  138 TRP
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  249 ASN
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  391 PHE
Chi-restraints excluded: chain B residue  392 TYR
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  402 THR
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  494 CYS
Chi-restraints excluded: chain B residue  519 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0370
   chunk 69 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.6258

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 238 ASN
A 545 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.140536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.126951 restraints weight = 24021.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.67
r_work: 0.3471 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7578  Z= 0.146
  Angle     :  1.034  26.226  10342  Z= 0.451
  Chirality :  0.182   1.727   1250
  Planarity :  0.005   0.050   1236
  Dihedral  :  8.079  76.018   1084
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 14.09 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.30), residues: 916
  helix:  1.60 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.48 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 108 
 TYR   0.009   0.001   TYR B 353 
 PHE   0.012   0.001   PHE A  35 
 TRP   0.011   0.001   TRP A  49 
 HIS   0.006   0.002   HIS A 556 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.15 ( 7576)
  covalent geometry    : angle       1.03247 /  0.45 (10336)
  hydrogen bonds       : bond        0.04316 /  2.75 (  446)
  hydrogen bonds       : angle       3.95054 /  2.80 ( 1296)
  link_NAG-ASN         : bond        0.00866 /  0.43 (    2)
  link_NAG-ASN         : angle       2.75135 /  1.24 (    6)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.7947 (ttm) cc_final: 0.7649 (ttm)
REVERT: A  201 ARG cc_start: 0.6910 (mmm160) cc_final: 0.6397 (mmm160)
REVERT: A  208 MET cc_start: 0.7148 (mmm) cc_final: 0.6918 (mmt)
REVERT: A  277 MET cc_start: 0.7523 (mtt) cc_final: 0.7301 (mtp)
REVERT: A  304 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6351 (mp0)
REVERT: A  312 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6273 (tt)
REVERT: A  376 LYS cc_start: 0.3098 (OUTLIER) cc_final: 0.2615 (mmtt)
REVERT: A  391 PHE cc_start: 0.4822 (OUTLIER) cc_final: 0.3743 (m-80)
REVERT: A  392 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.5435 (m-80)
REVERT: B  312 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7476 (tt)
REVERT: B  392 TYR cc_start: 0.3626 (OUTLIER) cc_final: 0.2868 (m-80)
REVERT: B  413 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7675 (tt)
  outliers start: 30
  outliers final: 21
  residues processed: 125
  average time/residue: 0.1304
  time to fit residues: 24.6089
Evaluate side-chains
  129 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   31 MET
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  376 LYS
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   60 SER
Chi-restraints excluded: chain B residue  106 HIS
Chi-restraints excluded: chain B residue  138 TRP
Chi-restraints excluded: chain B residue  249 ASN
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  392 TYR
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  402 THR
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  494 CYS
Chi-restraints excluded: chain B residue  519 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0980
   chunk 27 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 88 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 238 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.136527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.122804 restraints weight = 24444.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.68
r_work: 0.3451 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7578  Z= 0.165
  Angle     :  1.041  26.199  10342  Z= 0.457
  Chirality :  0.182   1.728   1250
  Planarity :  0.005   0.046   1236
  Dihedral  :  7.916  75.093   1081
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 14.59 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.30), residues: 916
  helix:  1.54 (0.21), residues: 670
  sheet:  None (None), residues: 0
  loop : -2.48 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 108 
 TYR   0.009   0.001   TYR B 353 
 PHE   0.013   0.001   PHE A  35 
 TRP   0.012   0.001   TRP A  49 
 HIS   0.006   0.002   HIS A 441 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00408 /  0.16 ( 7576)
  covalent geometry    : angle       1.03945 /  0.46 (10336)
  hydrogen bonds       : bond        0.04518 /  2.88 (  446)
  hydrogen bonds       : angle       3.97738 /  2.83 ( 1296)
  link_NAG-ASN         : bond        0.00873 /  0.44 (    2)
  link_NAG-ASN         : angle       2.75822 /  1.25 (    6)

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

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

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1832 Ramachandran restraints generated.
    916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.8000 (ttm) cc_final: 0.7704 (ttm)
REVERT: A  201 ARG cc_start: 0.6980 (mmm160) cc_final: 0.6442 (mmm160)
REVERT: A  208 MET cc_start: 0.7271 (mmm) cc_final: 0.7040 (mmt)
REVERT: A  277 MET cc_start: 0.7606 (mtt) cc_final: 0.7363 (mtp)
REVERT: A  304 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6301 (mp0)
REVERT: A  312 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6170 (tt)
REVERT: A  391 PHE cc_start: 0.4788 (OUTLIER) cc_final: 0.3738 (m-80)
REVERT: A  392 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.5440 (m-80)
REVERT: B  312 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7455 (tt)
REVERT: B  392 TYR cc_start: 0.3627 (OUTLIER) cc_final: 0.2841 (m-80)
REVERT: B  413 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7670 (tt)
  outliers start: 30
  outliers final: 23
  residues processed: 125
  average time/residue: 0.1416
  time to fit residues: 26.3657
Evaluate side-chains
  128 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 98
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   31 MET
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  304 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  376 LYS
Chi-restraints excluded: chain A residue  391 PHE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  494 CYS
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   60 SER
Chi-restraints excluded: chain B residue  106 HIS
Chi-restraints excluded: chain B residue  138 TRP
Chi-restraints excluded: chain B residue  227 THR
Chi-restraints excluded: chain B residue  249 ASN
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  392 TYR
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  402 THR
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  494 CYS
Chi-restraints excluded: chain B residue  519 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 82 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0980
   chunk 17 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 238 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.137846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.124022 restraints weight = 24296.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.69
r_work: 0.3468 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3346 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7578  Z= 0.142
  Angle     :  1.034  26.184  10342  Z= 0.451
  Chirality :  0.182   1.727   1250
  Planarity :  0.005   0.049   1236
  Dihedral  :  7.854  74.471   1081
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 14.59 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.30), residues: 916
  helix:  1.62 (0.21), residues: 670
  sheet:  None (None), residues: 0
  loop : -2.48 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 102 
 TYR   0.009   0.001   TYR B 353 
 PHE   0.012   0.001   PHE A  35 
 TRP   0.012   0.001   TRP A  49 
 HIS   0.006   0.002   HIS A 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.14 ( 7576)
  covalent geometry    : angle       1.03234 /  0.45 (10336)
  hydrogen bonds       : bond        0.04236 /  2.70 (  446)
  hydrogen bonds       : angle       3.93499 /  2.81 ( 1296)
  link_NAG-ASN         : bond        0.00852 /  0.43 (    2)
  link_NAG-ASN         : angle       2.74556 /  1.24 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3044.22 seconds
wall clock time: 52 minutes 22.65 seconds (3142.65 seconds total)