Starting phenix.real_space_refine
on Fri Jun  6 00:31:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r12_14228/06_2025/7r12_14228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r12_14228/06_2025/7r12_14228.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r12_14228/06_2025/7r12_14228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r12_14228/06_2025/7r12_14228.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r12_14228/06_2025/7r12_14228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r12_14228/06_2025/7r12_14228.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.089
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      39      5.16       5
     C    4383      2.51       5
     N    1130      2.21       5
     O    1305      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6858
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 4801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4801
          Classifications: {'peptide': 588}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1972
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 14, 'TRANS': 236}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 57
          Unusual residues: {' ZN': 1, 'NAG': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.42, per 1000 atoms: 0.64
  Number of scatterers: 6858
  At special positions: 0
  Unit cell: (75.46, 98.098, 139.062, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      39     16.00
     O    1305      8.00
     N    1130      7.00
     C    4383      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
      " NAG A1302 " - " ASN A 331 "
      " NAG D 902 " - " ASN D  53 "
      " NAG D 903 " - " ASN D  90 "
      " NAG D 904 " - " ASN D 103 "
      " NAG D 905 " - " ASN D 546 "
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 852.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D 901 "
        pdb="ZN    ZN D 901 " - pdb=" NE2 HIS D 378 "
        pdb="ZN    ZN D 901 " - pdb=" NE2 HIS D 374 "


  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1578

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 7 sheets defined
      52.1% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'D' and resid 20 through 53
      removed outlier: 4.441A  pdb=" N   ASP D  38 " --> pdb=" O   HIS D  34 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   LEU D  39 " --> pdb=" O   GLU D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 81
      removed outlier: 4.067A  pdb=" N   VAL D  59 " --> pdb=" O   THR D  55 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   GLN D  60 " --> pdb=" O   GLU D  56 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASN D  61 " --> pdb=" O   GLU D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 102
      removed outlier: 3.642A  pdb=" N   GLN D  96 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLN D 102 " --> pdb=" O   GLN D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 108
      removed outlier: 3.763A  pdb=" N   SER D 106 " --> pdb=" O   ASN D 103 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   VAL D 107 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 129
    Processing helix  chain 'D' and resid 146 through 155
      removed outlier: 3.523A  pdb=" N   ILE D 151 " --> pdb=" O   GLY D 147 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 194
      removed outlier: 3.556A  pdb=" N   TRP D 168 " --> pdb=" O   ALA D 164 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ARG D 169 " --> pdb=" O   TRP D 165 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   LYS D 174 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
      Proline residue:  D 178  - end of helix
      removed outlier: 3.594A  pdb=" N   GLU D 181 " --> pdb=" O   ARG D 177 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLU D 182 " --> pdb=" O   PRO D 178 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL D 185 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 226 through 231
    Processing helix  chain 'D' and resid 233 through 249
    Processing helix  chain 'D' and resid 275 through 280
      removed outlier: 4.059A  pdb=" N   SER D 280 " --> pdb=" O   ASN D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 293 through 300
    Processing helix  chain 'D' and resid 305 through 318
      removed outlier: 3.704A  pdb=" N   VAL D 318 " --> pdb=" O   PHE D 314 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 324 through 331
      removed outlier: 4.036A  pdb=" N   TRP D 328 " --> pdb=" O   THR D 324 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   GLU D 329 " --> pdb=" O   GLN D 325 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.700A  pdb=" N   HIS D 373 " --> pdb=" O   PHE D 369 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA D 384 " --> pdb=" O   GLN D 380 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   TYR D 385 " --> pdb=" O   TYR D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 386 through 388
      No H-bonds generated for 'chain 'D' and resid 386 through 388'
    Processing helix  chain 'D' and resid 389 through 393
      removed outlier: 3.618A  pdb=" N   ARG D 393 " --> pdb=" O   PHE D 390 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 399 through 412
      removed outlier: 3.970A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   SER D 409 " --> pdb=" O   GLY D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 422
    Processing helix  chain 'D' and resid 431 through 444
      removed outlier: 3.547A  pdb=" N   GLU D 435 " --> pdb=" O   ASP D 431 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 446 through 448
      No H-bonds generated for 'chain 'D' and resid 446 through 448'
    Processing helix  chain 'D' and resid 449 through 465
    Processing helix  chain 'D' and resid 472 through 484
      removed outlier: 3.602A  pdb=" N   LYS D 476 " --> pdb=" O   GLN D 472 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 499 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
      removed outlier: 3.543A  pdb=" N   THR D 517 " --> pdb=" O   ILE D 513 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ARG D 518 " --> pdb=" O   ARG D 514 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   THR D 519 " --> pdb=" O   TYR D 515 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE D 523 " --> pdb=" O   THR D 519 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 542
      removed outlier: 3.533A  pdb=" N   LYS D 541 " --> pdb=" O   PRO D 538 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 3.964A  pdb=" N   GLY D 551 " --> pdb=" O   SER D 547 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
      removed outlier: 4.081A  pdb=" N   VAL D 573 " --> pdb=" O   ALA D 569 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 581 through 588
      removed outlier: 3.622A  pdb=" N   PHE D 588 " --> pdb=" O   LEU D 584 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 588 through 599
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.617A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 4.216A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 390
      removed outlier: 3.696A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 3.862A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
      removed outlier: 3.525A  pdb=" N   TYR A 421 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.752A  pdb=" N   SER A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'D' and resid 131 through 132
    Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263
      removed outlier: 6.199A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 328
      removed outlier: 5.287A  pdb=" N   ILE A 584 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.643A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 453 through 454
    Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474

    301 hydrogen bonds defined for protein.
    846 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: 1.74

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2194
        1.34 -     1.46: 1719
        1.46 -     1.58: 3068
        1.58 -     1.70: 0
        1.70 -     1.81: 60
  Bond restraints: 7041
  Sorted by residual:
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.450 -0.044 2.00e-02 2.50e+03 4.78e+00
  bond pdb=" C1  NAG D 902 "
       pdb=" O5  NAG D 902 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.91e+00
  bond pdb=" C1  NAG A1302 "
       pdb=" O5  NAG A1302 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.85e+00
  bond pdb=" C1  NAG D 903 "
       pdb=" O5  NAG D 903 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.75e+00
  bond pdb=" C1  NAG D 904 "
       pdb=" O5  NAG D 904 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.68e+00
  ... (remaining 7036 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 9391
        1.72 -     3.44: 152
        3.44 -     5.15: 20
        5.15 -     6.87: 2
        6.87 -     8.59: 1
  Bond angle restraints: 9566
  Sorted by residual:
  angle pdb=" C   ASN D  90 "
        pdb=" N   LEU D  91 "
        pdb=" CA  LEU D  91 "
      ideal   model   delta    sigma   weight residual
     121.54  126.61   -5.07 1.91e+00 2.74e-01 7.05e+00
  angle pdb=" C   LEU D 423 "
        pdb=" N   LEU D 424 "
        pdb=" CA  LEU D 424 "
      ideal   model   delta    sigma   weight residual
     121.54  126.59   -5.05 1.91e+00 2.74e-01 7.00e+00
  angle pdb=" CA  LEU A 546 "
        pdb=" CB  LEU A 546 "
        pdb=" CG  LEU A 546 "
      ideal   model   delta    sigma   weight residual
     116.30  124.89   -8.59 3.50e+00 8.16e-02 6.02e+00
  angle pdb=" N   ILE D 421 "
        pdb=" CA  ILE D 421 "
        pdb=" C   ILE D 421 "
      ideal   model   delta    sigma   weight residual
     110.42  112.54   -2.12 9.60e-01 1.09e+00 4.87e+00
  angle pdb=" N   ASP D 427 "
        pdb=" CA  ASP D 427 "
        pdb=" C   ASP D 427 "
      ideal   model   delta    sigma   weight residual
     110.88  108.11    2.77 1.28e+00 6.10e-01 4.68e+00
  ... (remaining 9561 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 3824
       17.55 -    35.10: 336
       35.10 -    52.65: 66
       52.65 -    70.20: 12
       70.20 -    87.75: 4
  Dihedral angle restraints: 4242
    sinusoidal: 1787
      harmonic: 2455
  Sorted by residual:
  dihedral pdb=" CB  CYS D 530 "
           pdb=" SG  CYS D 530 "
           pdb=" SG  CYS D 542 "
           pdb=" CB  CYS D 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -119.56   33.56     1      1.00e+01 1.00e-02 1.60e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  123.28  -30.28     1      1.00e+01 1.00e-02 1.31e+01
  dihedral pdb=" CA  CYS D 344 "
           pdb=" C   CYS D 344 "
           pdb=" N   HIS D 345 "
           pdb=" CA  HIS D 345 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.88   16.12     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 4239 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 604
       0.030 -    0.060: 300
       0.060 -    0.089: 67
       0.089 -    0.119: 55
       0.119 -    0.149: 6
  Chirality restraints: 1032
  Sorted by residual:
  chirality pdb=" C1  NAG D 903 "
            pdb=" ND2 ASN D  90 "
            pdb=" C2  NAG D 903 "
            pdb=" O5  NAG D 903 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-01 2.50e+01 5.54e-01
  chirality pdb=" C1  NAG D 904 "
            pdb=" ND2 ASN D 103 "
            pdb=" C2  NAG D 904 "
            pdb=" O5  NAG D 904 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  VAL A 433 "
            pdb=" N   VAL A 433 "
            pdb=" C   VAL A 433 "
            pdb=" CB  VAL A 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  ... (remaining 1029 not shown)

  Planarity restraints: 1235
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 145 "   -0.033 5.00e-02 4.00e+02   4.99e-02 3.98e+00
        pdb=" N   PRO D 146 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO D 146 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D 146 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 234 "    0.030 5.00e-02 4.00e+02   4.61e-02 3.40e+00
        pdb=" N   PRO D 235 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO D 235 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D 235 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 578 "    0.020 5.00e-02 4.00e+02   3.10e-02 1.54e+00
        pdb=" N   PRO A 579 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 579 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 579 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1232 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 133
        2.71 -     3.26: 6429
        3.26 -     3.80: 10119
        3.80 -     4.35: 13356
        4.35 -     4.90: 23311
  Nonbonded interactions: 53348
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D 183 "
            pdb=" OD1 ASP D 509 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OE2 GLU D 402 "
            pdb="ZN    ZN D 901 "
     model   vdw
     2.211 2.230
  nonbonded pdb=" O   ARG A 408 "
            pdb=" NE2 GLN A 414 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   ASP A 442 "
            pdb=" ND2 ASN A 448 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" OE1 GLU A 406 "
            pdb=" OH  TYR A 495 "
     model   vdw
     2.325 3.040
  ... (remaining 53343 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             17.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.520
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
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      :  0.003   0.044   7057  Z= 0.156
  Angle     :  0.568   9.935   9600  Z= 0.287
  Chirality :  0.041   0.149   1032
  Planarity :  0.004   0.050   1229
  Dihedral  : 13.554  87.747   2640
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.29), residues: 831
  helix:  1.22 (0.28), residues: 374
  sheet:  0.95 (0.60), residues: 70
  loop : -0.81 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 353 
 HIS   0.005   0.001   HIS D 401 
 PHE   0.011   0.001   PHE D 308 
 TYR   0.021   0.001   TYR D 199 
 ARG   0.002   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00808 (    6)
  link_NAG-ASN         : angle       3.41144 (   18)
  hydrogen bonds       : bond        0.13672 (  301)
  hydrogen bonds       : angle       5.46514 (  846)
  metal coordination   : bond        0.00301 (    2)
  SS BOND              : bond        0.00240 (    8)
  SS BOND              : angle       0.70262 (   16)
  covalent geometry    : bond        0.00345 ( 7041)
  covalent geometry    : angle       0.54902 ( 9566)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.700 
Fit side-chains
REVERT: D  160 GLU cc_start: 0.6626 (tt0) cc_final: 0.6374 (tt0)
REVERT: D  470 LYS cc_start: 0.7909 (mttt) cc_final: 0.7490 (mmtm)
REVERT: A  420 ASP cc_start: 0.8332 (m-30) cc_final: 0.7965 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1792
  time to fit residues: 22.7436
Evaluate side-chains
  79 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.151743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.124694 restraints weight = 7097.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.20
r_work: 0.3134 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.0746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7057  Z= 0.179
  Angle     :  0.583  10.685   9600  Z= 0.290
  Chirality :  0.043   0.153   1032
  Planarity :  0.004   0.049   1229
  Dihedral  :  6.130  59.726   1032
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  4.74 %
    Favored  : 93.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.29), residues: 831
  helix:  1.23 (0.28), residues: 383
  sheet:  0.91 (0.60), residues: 70
  loop : -0.77 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 566 
 HIS   0.003   0.001   HIS D 401 
 PHE   0.017   0.002   PHE D 327 
 TYR   0.020   0.002   TYR D 183 
 ARG   0.002   0.000   ARG A 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00696 (    6)
  link_NAG-ASN         : angle       3.71832 (   18)
  hydrogen bonds       : bond        0.05528 (  301)
  hydrogen bonds       : angle       4.51732 (  846)
  metal coordination   : bond        0.00423 (    2)
  SS BOND              : bond        0.00298 (    8)
  SS BOND              : angle       0.86532 (   16)
  covalent geometry    : bond        0.00437 ( 7041)
  covalent geometry    : angle       0.56068 ( 9566)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.771 
Fit side-chains
REVERT: D  160 GLU cc_start: 0.7222 (tt0) cc_final: 0.6792 (tt0)
REVERT: D  470 LYS cc_start: 0.8107 (mttt) cc_final: 0.7480 (mmtm)
REVERT: A  420 ASP cc_start: 0.8815 (m-30) cc_final: 0.8273 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 91
  average time/residue: 0.1672
  time to fit residues: 21.4367
Evaluate side-chains
  84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  363 LYS
Chi-restraints excluded: chain D residue  367 ASP
Chi-restraints excluded: chain D residue  474 MET
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  549 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 49 optimal weight:    0.2980
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    0.3980
   chunk 71 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.152185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.125619 restraints weight = 7212.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 1.21
r_work: 0.2928 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.0911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7057  Z= 0.160
  Angle     :  0.535   6.592   9600  Z= 0.272
  Chirality :  0.042   0.154   1032
  Planarity :  0.004   0.048   1229
  Dihedral  :  5.353  54.995   1032
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  6.36 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.29), residues: 831
  helix:  1.25 (0.28), residues: 384
  sheet:  0.97 (0.60), residues: 70
  loop : -0.72 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 566 
 HIS   0.003   0.001   HIS D 540 
 PHE   0.015   0.001   PHE D 327 
 TYR   0.018   0.002   TYR D 183 
 ARG   0.002   0.000   ARG D 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00174 (    6)
  link_NAG-ASN         : angle       1.48142 (   18)
  hydrogen bonds       : bond        0.05218 (  301)
  hydrogen bonds       : angle       4.39641 (  846)
  metal coordination   : bond        0.00395 (    2)
  SS BOND              : bond        0.00341 (    8)
  SS BOND              : angle       0.86341 (   16)
  covalent geometry    : bond        0.00390 ( 7041)
  covalent geometry    : angle       0.53098 ( 9566)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.808 
Fit side-chains
REVERT: D  160 GLU cc_start: 0.7173 (tt0) cc_final: 0.6815 (tt0)
REVERT: D  470 LYS cc_start: 0.8135 (mttt) cc_final: 0.7481 (mmtm)
REVERT: A  420 ASP cc_start: 0.8779 (m-30) cc_final: 0.8259 (m-30)
  outliers start: 14
  outliers final: 10
  residues processed: 91
  average time/residue: 0.1745
  time to fit residues: 23.0582
Evaluate side-chains
  88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  198 ASP
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  367 ASP
Chi-restraints excluded: chain D residue  420 SER
Chi-restraints excluded: chain D residue  474 MET
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  549 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 69 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
D  51 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.151687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.122962 restraints weight = 7293.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.36
r_work: 0.2886 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7057  Z= 0.166
  Angle     :  0.560   7.540   9600  Z= 0.284
  Chirality :  0.043   0.271   1032
  Planarity :  0.004   0.049   1229
  Dihedral  :  4.943  56.971   1032
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  7.58 %
    Favored  : 90.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.29), residues: 831
  helix:  1.27 (0.28), residues: 384
  sheet:  0.80 (0.61), residues: 70
  loop : -0.72 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 566 
 HIS   0.003   0.001   HIS D 540 
 PHE   0.015   0.001   PHE D 327 
 TYR   0.017   0.002   TYR D 183 
 ARG   0.002   0.000   ARG D 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    6)
  link_NAG-ASN         : angle       2.04890 (   18)
  hydrogen bonds       : bond        0.05273 (  301)
  hydrogen bonds       : angle       4.42181 (  846)
  metal coordination   : bond        0.00421 (    2)
  SS BOND              : bond        0.00604 (    8)
  SS BOND              : angle       2.09696 (   16)
  covalent geometry    : bond        0.00407 ( 7041)
  covalent geometry    : angle       0.54717 ( 9566)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.706 
Fit side-chains
REVERT: D  160 GLU cc_start: 0.7233 (tt0) cc_final: 0.6832 (tt0)
REVERT: D  175 GLN cc_start: 0.7126 (mt0) cc_final: 0.6757 (mt0)
REVERT: D  470 LYS cc_start: 0.8091 (mttt) cc_final: 0.7470 (mptt)
REVERT: A  420 ASP cc_start: 0.8809 (m-30) cc_final: 0.8307 (m-30)
  outliers start: 14
  outliers final: 12
  residues processed: 90
  average time/residue: 0.1614
  time to fit residues: 20.5631
Evaluate side-chains
  93 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  198 ASP
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  420 SER
Chi-restraints excluded: chain D residue  474 MET
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  549 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0060
   chunk 28 optimal weight:    0.5980
   chunk 9 optimal weight:    4.9990
   chunk 63 optimal weight:    0.2980
   chunk 2 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0970
   overall best weight:    0.3194

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 414 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.154662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.129569 restraints weight = 7194.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.19
r_work: 0.2956 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   7057  Z= 0.119
  Angle     :  0.518  11.169   9600  Z= 0.260
  Chirality :  0.042   0.287   1032
  Planarity :  0.004   0.048   1229
  Dihedral  :  4.650  56.936   1032
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.93 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.29), residues: 831
  helix:  1.48 (0.28), residues: 384
  sheet:  1.04 (0.62), residues: 71
  loop : -0.50 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS D 241 
 PHE   0.010   0.001   PHE D 327 
 TYR   0.017   0.001   TYR D 183 
 ARG   0.001   0.000   ARG A 577 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00355 (    6)
  link_NAG-ASN         : angle       2.13921 (   18)
  hydrogen bonds       : bond        0.04389 (  301)
  hydrogen bonds       : angle       4.22046 (  846)
  metal coordination   : bond        0.00243 (    2)
  SS BOND              : bond        0.00753 (    8)
  SS BOND              : angle       2.22694 (   16)
  covalent geometry    : bond        0.00282 ( 7041)
  covalent geometry    : angle       0.50221 ( 9566)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.779 
Fit side-chains
REVERT: D  160 GLU cc_start: 0.7132 (tt0) cc_final: 0.6742 (tt0)
REVERT: D  175 GLN cc_start: 0.7088 (mt0) cc_final: 0.6749 (mt0)
REVERT: A  420 ASP cc_start: 0.8767 (m-30) cc_final: 0.8322 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 85
  average time/residue: 0.1806
  time to fit residues: 21.5441
Evaluate side-chains
  86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  198 ASP
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  420 SER
Chi-restraints excluded: chain D residue  474 MET
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  440 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0020
   chunk 69 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 43 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 59 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.4788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.152793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.124087 restraints weight = 7260.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.35
r_work: 0.2908 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.1141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   7057  Z= 0.146
  Angle     :  0.546  12.981   9600  Z= 0.275
  Chirality :  0.042   0.291   1032
  Planarity :  0.004   0.048   1229
  Dihedral  :  4.708  57.259   1032
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 10.15 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.29), residues: 831
  helix:  1.44 (0.28), residues: 386
  sheet:  1.02 (0.62), residues: 71
  loop : -0.55 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 566 
 HIS   0.003   0.001   HIS D 540 
 PHE   0.014   0.001   PHE D 327 
 TYR   0.016   0.001   TYR D 183 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00190 (    6)
  link_NAG-ASN         : angle       1.95934 (   18)
  hydrogen bonds       : bond        0.04845 (  301)
  hydrogen bonds       : angle       4.24817 (  846)
  metal coordination   : bond        0.00319 (    2)
  SS BOND              : bond        0.00768 (    8)
  SS BOND              : angle       2.31884 (   16)
  covalent geometry    : bond        0.00359 ( 7041)
  covalent geometry    : angle       0.53203 ( 9566)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.816 
Fit side-chains
REVERT: D  160 GLU cc_start: 0.7199 (tt0) cc_final: 0.6787 (tt0)
REVERT: D  175 GLN cc_start: 0.7084 (mt0) cc_final: 0.6678 (mt0)
REVERT: D  470 LYS cc_start: 0.8016 (mttt) cc_final: 0.7361 (mmtm)
REVERT: A  389 ASP cc_start: 0.7127 (m-30) cc_final: 0.6841 (p0)
REVERT: A  405 ASP cc_start: 0.8033 (m-30) cc_final: 0.7687 (m-30)
REVERT: A  420 ASP cc_start: 0.8793 (m-30) cc_final: 0.8307 (m-30)
  outliers start: 14
  outliers final: 12
  residues processed: 90
  average time/residue: 0.2015
  time to fit residues: 25.7421
Evaluate side-chains
  91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 1.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  198 ASP
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  420 SER
Chi-restraints excluded: chain D residue  474 MET
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  549 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0980
   chunk 0 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.152510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.123450 restraints weight = 7185.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.31
r_work: 0.3143 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   7057  Z= 0.149
  Angle     :  0.554  14.315   9600  Z= 0.279
  Chirality :  0.042   0.284   1032
  Planarity :  0.004   0.048   1229
  Dihedral  :  4.736  57.436   1032
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 10.83 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.29), residues: 831
  helix:  1.41 (0.28), residues: 387
  sheet:  1.10 (0.62), residues: 71
  loop : -0.53 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 353 
 HIS   0.003   0.001   HIS D 540 
 PHE   0.014   0.001   PHE D 327 
 TYR   0.016   0.001   TYR D  50 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00179 (    6)
  link_NAG-ASN         : angle       1.84060 (   18)
  hydrogen bonds       : bond        0.04931 (  301)
  hydrogen bonds       : angle       4.24720 (  846)
  metal coordination   : bond        0.00360 (    2)
  SS BOND              : bond        0.00793 (    8)
  SS BOND              : angle       2.26641 (   16)
  covalent geometry    : bond        0.00367 ( 7041)
  covalent geometry    : angle       0.54128 ( 9566)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.716 
Fit side-chains
REVERT: D  160 GLU cc_start: 0.7193 (tt0) cc_final: 0.6793 (tt0)
REVERT: D  175 GLN cc_start: 0.7201 (mt0) cc_final: 0.6769 (mt0)
REVERT: D  470 LYS cc_start: 0.8055 (mttt) cc_final: 0.7381 (mmtm)
REVERT: D  568 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8102 (tt)
REVERT: A  405 ASP cc_start: 0.8112 (m-30) cc_final: 0.7750 (m-30)
REVERT: A  420 ASP cc_start: 0.8805 (m-30) cc_final: 0.8317 (m-30)
  outliers start: 13
  outliers final: 12
  residues processed: 85
  average time/residue: 0.2159
  time to fit residues: 26.8893
Evaluate side-chains
  90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  198 ASP
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  420 SER
Chi-restraints excluded: chain D residue  474 MET
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  549 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 66 optimal weight:    0.4980
   chunk 33 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0980
   chunk 65 optimal weight:    0.5980
   chunk 34 optimal weight:    0.2980
   overall best weight:    0.4380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.152992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.123633 restraints weight = 7225.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 1.32
r_work: 0.3129 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   7057  Z= 0.137
  Angle     :  0.538  13.156   9600  Z= 0.270
  Chirality :  0.042   0.263   1032
  Planarity :  0.004   0.048   1229
  Dihedral  :  4.688  57.646   1032
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 10.96 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.29), residues: 831
  helix:  1.49 (0.28), residues: 383
  sheet:  1.09 (0.62), residues: 71
  loop : -0.48 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 566 
 HIS   0.002   0.001   HIS D 540 
 PHE   0.012   0.001   PHE D 327 
 TYR   0.016   0.001   TYR D 183 
 ARG   0.001   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00160 (    6)
  link_NAG-ASN         : angle       1.76488 (   18)
  hydrogen bonds       : bond        0.04745 (  301)
  hydrogen bonds       : angle       4.20174 (  846)
  metal coordination   : bond        0.00283 (    2)
  SS BOND              : bond        0.00717 (    8)
  SS BOND              : angle       2.13043 (   16)
  covalent geometry    : bond        0.00334 ( 7041)
  covalent geometry    : angle       0.52608 ( 9566)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 2.766 
Fit side-chains
REVERT: D  160 GLU cc_start: 0.7176 (tt0) cc_final: 0.6765 (tt0)
REVERT: D  175 GLN cc_start: 0.7160 (mt0) cc_final: 0.6741 (mt0)
REVERT: D  568 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8095 (tt)
REVERT: A  405 ASP cc_start: 0.8088 (m-30) cc_final: 0.7749 (m-30)
REVERT: A  420 ASP cc_start: 0.8791 (m-30) cc_final: 0.8306 (m-30)
  outliers start: 14
  outliers final: 12
  residues processed: 86
  average time/residue: 0.2240
  time to fit residues: 28.0458
Evaluate side-chains
  90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  198 ASP
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  420 SER
Chi-restraints excluded: chain D residue  474 MET
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  549 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0770
   chunk 46 optimal weight:    0.1980
   chunk 21 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0020
   chunk 48 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.3746

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.153944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.126350 restraints weight = 7266.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.25
r_work: 0.2972 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   7057  Z= 0.127
  Angle     :  0.533  14.541   9600  Z= 0.269
  Chirality :  0.041   0.258   1032
  Planarity :  0.004   0.048   1229
  Dihedral  :  4.664  57.590   1032
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.37 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.29), residues: 831
  helix:  1.48 (0.28), residues: 383
  sheet:  1.08 (0.63), residues: 70
  loop : -0.43 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 353 
 HIS   0.003   0.001   HIS D 540 
 PHE   0.011   0.001   PHE D 327 
 TYR   0.027   0.001   TYR D  50 
 ARG   0.001   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00152 (    6)
  link_NAG-ASN         : angle       1.67470 (   18)
  hydrogen bonds       : bond        0.04589 (  301)
  hydrogen bonds       : angle       4.18546 (  846)
  metal coordination   : bond        0.00261 (    2)
  SS BOND              : bond        0.00738 (    8)
  SS BOND              : angle       2.02692 (   16)
  covalent geometry    : bond        0.00306 ( 7041)
  covalent geometry    : angle       0.52275 ( 9566)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 1.528 
Fit side-chains
REVERT: D  160 GLU cc_start: 0.7118 (tt0) cc_final: 0.6759 (tt0)
REVERT: D  175 GLN cc_start: 0.7183 (mt0) cc_final: 0.6870 (mt0)
REVERT: D  568 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8113 (tt)
REVERT: A  405 ASP cc_start: 0.7738 (m-30) cc_final: 0.7456 (m-30)
REVERT: A  420 ASP cc_start: 0.8749 (m-30) cc_final: 0.8272 (m-30)
  outliers start: 12
  outliers final: 11
  residues processed: 85
  average time/residue: 0.2318
  time to fit residues: 27.8976
Evaluate side-chains
  88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  198 ASP
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  420 SER
Chi-restraints excluded: chain D residue  474 MET
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  445 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 30 optimal weight:    0.0010
   chunk 62 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 34 optimal weight:    0.6980
   chunk 14 optimal weight:    0.3980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.4386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.163674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.149969 restraints weight = 7294.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 0.69
r_work: 0.3132 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.1249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   7057  Z= 0.136
  Angle     :  0.539  14.252   9600  Z= 0.271
  Chirality :  0.042   0.252   1032
  Planarity :  0.004   0.048   1229
  Dihedral  :  4.670  57.542   1032
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 10.96 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.29), residues: 831
  helix:  1.49 (0.28), residues: 383
  sheet:  1.08 (0.63), residues: 70
  loop : -0.45 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 353 
 HIS   0.003   0.001   HIS D 540 
 PHE   0.013   0.001   PHE D 327 
 TYR   0.016   0.001   TYR D  50 
 ARG   0.001   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00165 (    6)
  link_NAG-ASN         : angle       1.73626 (   18)
  hydrogen bonds       : bond        0.04751 (  301)
  hydrogen bonds       : angle       4.18993 (  846)
  metal coordination   : bond        0.00289 (    2)
  SS BOND              : bond        0.00731 (    8)
  SS BOND              : angle       2.00953 (   16)
  covalent geometry    : bond        0.00332 ( 7041)
  covalent geometry    : angle       0.52815 ( 9566)

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

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

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1662 Ramachandran restraints generated.
    831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: D  175 GLN cc_start: 0.7174 (mt0) cc_final: 0.6853 (mt0)
REVERT: D  568 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8026 (tt)
REVERT: A  405 ASP cc_start: 0.7827 (m-30) cc_final: 0.7543 (m-30)
REVERT: A  420 ASP cc_start: 0.8746 (m-30) cc_final: 0.8256 (m-30)
  outliers start: 14
  outliers final: 12
  residues processed: 88
  average time/residue: 0.1654
  time to fit residues: 20.8672
Evaluate side-chains
  92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  198 ASP
Chi-restraints excluded: chain D residue  283 VAL
Chi-restraints excluded: chain D residue  347 THR
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  420 SER
Chi-restraints excluded: chain D residue  474 MET
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  549 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 15 optimal weight:    0.0570
   chunk 82 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   chunk 60 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.5498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.162267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.148630 restraints weight = 7228.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 0.63
r_work: 0.3336 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.1280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   7057  Z= 0.158
  Angle     :  0.564  14.202   9600  Z= 0.283
  Chirality :  0.042   0.255   1032
  Planarity :  0.004   0.048   1229
  Dihedral  :  4.786  58.419   1032
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.10 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.29), residues: 831
  helix:  1.35 (0.28), residues: 390
  sheet:  1.05 (0.63), residues: 70
  loop : -0.55 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 353 
 HIS   0.003   0.001   HIS D 540 
 PHE   0.015   0.001   PHE D 327 
 TYR   0.016   0.002   TYR D 183 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00177 (    6)
  link_NAG-ASN         : angle       1.87042 (   18)
  hydrogen bonds       : bond        0.05131 (  301)
  hydrogen bonds       : angle       4.25329 (  846)
  metal coordination   : bond        0.00403 (    2)
  SS BOND              : bond        0.00753 (    8)
  SS BOND              : angle       2.04480 (   16)
  covalent geometry    : bond        0.00389 ( 7041)
  covalent geometry    : angle       0.55281 ( 9566)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4024.26 seconds
wall clock time: 72 minutes 47.10 seconds (4367.10 seconds total)