Starting phenix.real_space_refine
on Tue May 13 19:49:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jyp_36729/05_2025/8jyp_36729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jyp_36729/05_2025/8jyp_36729.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jyp_36729/05_2025/8jyp_36729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jyp_36729/05_2025/8jyp_36729.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jyp_36729/05_2025/8jyp_36729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jyp_36729/05_2025/8jyp_36729.cif"
  }
  resolution = 3.38
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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 4890 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: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4235      2.51       5
     N    1081      2.21       5
     O    1274      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6627
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 199, 1581
          Classifications: {'peptide': 199}
          Link IDs: {'PTRANS': 14, 'TRANS': 184}
    Chain: "D"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.88, per 1000 atoms: 0.89
  Number of scatterers: 6627
  At special positions: 0
  Unit cell: (99.495, 80.4, 124.62, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1274      8.00
     N    1081      7.00
     C    4235      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    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=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.04
    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

  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
    ALPHA1-3
      " BMA E   3 " - " MAN E   4 "
    ALPHA1-6
      " BMA E   3 " - " MAN E   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
      " NAG B   1 " - " ASN D 546 "
      " NAG C   1 " - " ASN D  90 "
      " NAG D 701 " - " ASN D 322 "
      " NAG D 702 " - " ASN D 432 "
      " NAG D 703 " - " ASN D  53 "
      " NAG E   1 " - " ASN D 103 "
  Time building additional restraints: 2.09
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 6 sheets defined
      53.2% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 367 through 371
    Processing helix  chain 'A' and resid 403 through 410
      removed outlier: 3.566A  pdb=" N   GLU A 406 " --> pdb=" O   ARG A 403 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   VAL A 407 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   SER A 408 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'D' and resid 20 through 53
      removed outlier: 3.560A  pdb=" N   GLN D  24 " --> pdb=" O   THR D  20 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   HIS D  34 " --> pdb=" O   ASP D  30 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ASP D  38 " --> pdb=" O   HIS D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 80
    Processing helix  chain 'D' and resid 81 through 83
      No H-bonds generated for 'chain 'D' and resid 81 through 83'
    Processing helix  chain 'D' and resid 84 through 88
      removed outlier: 3.851A  pdb=" N   GLU D  87 " --> pdb=" O   PRO D  84 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ILE D  88 " --> pdb=" O   LEU D  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 84 through 88'
    Processing helix  chain 'D' and resid 92 through 104
      removed outlier: 3.666A  pdb=" N   GLN D  96 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLY D 104 " --> pdb=" O   LEU D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 130
    Processing helix  chain 'D' and resid 147 through 155
    Processing helix  chain 'D' and resid 157 through 194
      removed outlier: 3.652A  pdb=" N   ARG D 169 " --> pdb=" O   TRP D 165 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LYS D 174 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
      removed outlier: 5.001A  pdb=" N   GLN D 175 " --> pdb=" O   GLU D 171 " (cutoff:3.500A)
      Proline residue:  D 178  - end of helix
      removed outlier: 3.837A  pdb=" N   VAL D 185 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASN D 194 " --> pdb=" O   MET D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'D' and resid 220 through 233
      removed outlier: 3.933A  pdb=" N   GLU D 224 " --> pdb=" O   GLY D 220 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU D 232 " --> pdb=" O   HIS D 228 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE D 233 " --> pdb=" O   THR D 229 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 252
      removed outlier: 3.534A  pdb=" N   TYR D 237 " --> pdb=" O   ILE D 233 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ASN D 250 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ALA D 251 " --> pdb=" O   LYS D 247 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 279
    Processing helix  chain 'D' and resid 293 through 300
    Processing helix  chain 'D' and resid 303 through 318
      removed outlier: 3.831A  pdb=" N   VAL D 318 " --> pdb=" O   PHE D 314 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 324 through 331
      removed outlier: 3.617A  pdb=" N   TRP D 328 " --> pdb=" O   THR D 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.733A  pdb=" N   HIS D 373 " --> pdb=" O   PHE D 369 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   HIS D 378 " --> pdb=" O   HIS D 374 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TYR D 385 " --> pdb=" O   TYR D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 399 through 413
      removed outlier: 4.236A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   SER D 409 " --> pdb=" O   GLY D 405 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU D 410 " --> pdb=" O   GLU D 406 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   SER D 411 " --> pdb=" O   ILE D 407 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 422
    Processing helix  chain 'D' and resid 431 through 447
      removed outlier: 3.574A  pdb=" N   GLU D 435 " --> pdb=" O   ASP D 431 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   THR D 445 " --> pdb=" O   LYS D 441 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 466
      removed outlier: 4.328A  pdb=" N   PHE D 452 " --> pdb=" O   GLY D 448 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 469 through 471
      No H-bonds generated for 'chain 'D' and resid 469 through 471'
    Processing helix  chain 'D' and resid 472 through 482
    Processing helix  chain 'D' and resid 498 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
      removed outlier: 4.218A  pdb=" N   THR D 519 " --> pdb=" O   TYR D 515 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU D 520 " --> pdb=" O   TYR D 516 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   PHE D 523 " --> pdb=" O   THR D 519 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLN D 524 " --> pdb=" O   LEU D 520 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 548 through 559
      removed outlier: 3.677A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 572
    Processing helix  chain 'D' and resid 581 through 599
      Proline residue:  D 590  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.944A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
      removed outlier: 3.671A  pdb=" N   TYR A 453 " --> pdb=" O   GLN A 493 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.726A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 132
      removed outlier: 3.698A  pdb=" N   VAL D 132 " --> pdb=" O   LEU D 142 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LEU D 142 " --> pdb=" O   VAL D 132 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263
      removed outlier: 5.796A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 350

    284 hydrogen bonds defined for protein.
    810 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: 1.80

  Time building geometry restraints manager: 2.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2091
        1.34 -     1.46: 1769
        1.46 -     1.58: 2895
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6813
  Sorted by residual:
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 2.98e+00
  bond pdb=" CA  LEU D 351 "
       pdb=" C   LEU D 351 "
    ideal  model  delta    sigma   weight residual
    1.523  1.500  0.022 1.41e-02 5.03e+03 2.47e+00
  bond pdb=" C1  MAN E   4 "
       pdb=" C2  MAN E   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.556 -0.030 2.00e-02 2.50e+03 2.30e+00
  bond pdb=" C1  BMA C   3 "
       pdb=" C2  BMA C   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.549 -0.030 2.00e-02 2.50e+03 2.24e+00
  bond pdb=" C1  NAG D 703 "
       pdb=" O5  NAG D 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.13e+00
  ... (remaining 6808 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 8980
        1.56 -     3.12: 221
        3.12 -     4.68: 42
        4.68 -     6.24: 15
        6.24 -     7.81: 4
  Bond angle restraints: 9262
  Sorted by residual:
  angle pdb=" C   HIS D  34 "
        pdb=" N   GLU D  35 "
        pdb=" CA  GLU D  35 "
      ideal   model   delta    sigma   weight residual
     120.31  114.89    5.42 1.52e+00 4.33e-01 1.27e+01
  angle pdb=" C   GLU D 182 "
        pdb=" N   TYR D 183 "
        pdb=" CA  TYR D 183 "
      ideal   model   delta    sigma   weight residual
     120.44  124.57   -4.13 1.30e+00 5.92e-01 1.01e+01
  angle pdb=" C   PRO D 135 "
        pdb=" N   ASP D 136 "
        pdb=" CA  ASP D 136 "
      ideal   model   delta    sigma   weight residual
     121.54  127.00   -5.46 1.91e+00 2.74e-01 8.17e+00
  angle pdb=" C   ALA A 344 "
        pdb=" N   THR A 345 "
        pdb=" CA  THR A 345 "
      ideal   model   delta    sigma   weight residual
     121.54  126.77   -5.23 1.91e+00 2.74e-01 7.51e+00
  angle pdb=" C   ASN D 432 "
        pdb=" CA  ASN D 432 "
        pdb=" CB  ASN D 432 "
      ideal   model   delta    sigma   weight residual
     110.84  106.66    4.18 1.66e+00 3.63e-01 6.35e+00
  ... (remaining 9257 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.77: 3930
       21.77 -    43.54: 234
       43.54 -    65.31: 16
       65.31 -    87.08: 18
       87.08 -   108.85: 8
  Dihedral angle restraints: 4206
    sinusoidal: 1870
      harmonic: 2336
  Sorted by residual:
  dihedral pdb=" CB  CYS D 133 "
           pdb=" SG  CYS D 133 "
           pdb=" SG  CYS D 141 "
           pdb=" CB  CYS D 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   36.06   56.94     1      1.00e+01 1.00e-02 4.36e+01
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.77   55.77     1      1.00e+01 1.00e-02 4.20e+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   46.67   46.33     1      1.00e+01 1.00e-02 2.97e+01
  ... (remaining 4203 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 998
       0.125 -    0.250: 7
       0.250 -    0.375: 5
       0.375 -    0.500: 0
       0.500 -    0.625: 1
  Chirality restraints: 1011
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN D 103 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.78   -0.62 2.00e-01 2.50e+01 9.76e+00
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN D 546 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.92e+00
  ... (remaining 1008 not shown)

  Planarity restraints: 1186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 163 "    0.016 2.00e-02 2.50e+03   1.16e-02 3.34e+00
        pdb=" CG  TRP D 163 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 163 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 163 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 163 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 163 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 163 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 163 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 163 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 163 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 103 "    0.016 2.00e-02 2.50e+03   1.57e-02 3.08e+00
        pdb=" CG  ASN D 103 "   -0.013 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 103 "   -0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 103 "   -0.021 2.00e-02 2.50e+03
        pdb=" C1  NAG E   1 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 372 "   -0.025 5.00e-02 4.00e+02   3.82e-02 2.33e+00
        pdb=" N   PRO A 373 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 373 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 373 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1183 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1896
        2.81 -     3.33: 6469
        3.33 -     3.86: 10683
        3.86 -     4.38: 11942
        4.38 -     4.90: 20760
  Nonbonded interactions: 51750
  Sorted by model distance:
  nonbonded pdb=" O   ASP D 499 "
            pdb=" OG  SER D 502 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OG1 THR A 500 "
            pdb=" OH  TYR D  41 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OG  SER D 611 "
            pdb=" O   ALA D 614 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   GLY D 268 "
            pdb=" ND2 ASN D 277 "
     model   vdw
     2.315 3.120
  nonbonded pdb=" OD1 ASP D 494 "
            pdb=" OG1 THR D 496 "
     model   vdw
     2.322 3.040
  ... (remaining 51745 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:             5.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.080
  Process input model:                     21.270
  Find NCS groups from input model:        0.070
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
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   0.035   6834  Z= 0.166
  Angle     :  0.653   8.739   9318  Z= 0.319
  Chirality :  0.051   0.625   1011
  Planarity :  0.003   0.038   1179
  Dihedral  : 14.643 108.849   2685
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.31), residues: 791
  helix:  1.06 (0.27), residues: 394
  sheet:  1.22 (0.77), residues: 44
  loop : -0.77 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP D 163 
 HIS   0.003   0.001   HIS D  34 
 PHE   0.016   0.001   PHE D  32 
 TYR   0.011   0.001   TYR A 453 
 ARG   0.001   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00921 (    7)
  link_NAG-ASN         : angle       3.83877 (   21)
  link_ALPHA1-6        : bond        0.00367 (    1)
  link_ALPHA1-6        : angle       1.63473 (    3)
  link_BETA1-4         : bond        0.00286 (    5)
  link_BETA1-4         : angle       1.86959 (   15)
  link_ALPHA1-3        : bond        0.00328 (    1)
  link_ALPHA1-3        : angle       1.52227 (    3)
  hydrogen bonds       : bond        0.16587 (  284)
  hydrogen bonds       : angle       6.03160 (  810)
  SS BOND              : bond        0.00326 (    7)
  SS BOND              : angle       0.78482 (   14)
  covalent geometry    : bond        0.00330 ( 6813)
  covalent geometry    : angle       0.62191 ( 9262)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: A  493 GLN cc_start: 0.8999 (tp40) cc_final: 0.8665 (tp-100)
REVERT: D  270 MET cc_start: 0.8223 (tpt) cc_final: 0.7974 (tpp)
REVERT: D  474 MET cc_start: 0.8654 (mmp) cc_final: 0.8451 (mmp)
REVERT: D  531 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8653 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1441
  time to fit residues: 10.6825
Evaluate side-chains
  38 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0770
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    1.7344

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
** D  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.069133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.047969 restraints weight = 25634.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 4.38
r_work: 0.2672 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6834  Z= 0.219
  Angle     :  0.642   8.101   9318  Z= 0.311
  Chirality :  0.046   0.299   1011
  Planarity :  0.004   0.034   1179
  Dihedral  : 10.052  73.904   1148
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  5.59 %
    Favored  : 93.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.70 (0.31), residues: 791
  helix:  1.61 (0.27), residues: 391
  sheet:  0.79 (0.77), residues: 44
  loop : -0.88 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP D 163 
 HIS   0.004   0.001   HIS D 535 
 PHE   0.010   0.001   PHE D 369 
 TYR   0.017   0.001   TYR A 453 
 ARG   0.003   0.000   ARG D 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00837 (    7)
  link_NAG-ASN         : angle       3.63803 (   21)
  link_ALPHA1-6        : bond        0.00169 (    1)
  link_ALPHA1-6        : angle       2.21401 (    3)
  link_BETA1-4         : bond        0.00572 (    5)
  link_BETA1-4         : angle       2.13189 (   15)
  link_ALPHA1-3        : bond        0.00908 (    1)
  link_ALPHA1-3        : angle       2.27270 (    3)
  hydrogen bonds       : bond        0.05773 (  284)
  hydrogen bonds       : angle       4.58179 (  810)
  SS BOND              : bond        0.00329 (    7)
  SS BOND              : angle       0.91068 (   14)
  covalent geometry    : bond        0.00491 ( 6813)
  covalent geometry    : angle       0.61040 ( 9262)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A  493 GLN cc_start: 0.9147 (tp40) cc_final: 0.8879 (tp-100)
REVERT: D  108 LEU cc_start: 0.9204 (mm) cc_final: 0.8908 (tp)
REVERT: D  270 MET cc_start: 0.8565 (tpt) cc_final: 0.8224 (tpp)
REVERT: D  462 MET cc_start: 0.9389 (mmp) cc_final: 0.9163 (mtm)
REVERT: D  531 GLN cc_start: 0.9379 (tm-30) cc_final: 0.9055 (tm-30)
  outliers start: 5
  outliers final: 2
  residues processed: 36
  average time/residue: 0.1470
  time to fit residues: 8.4228
Evaluate side-chains
  34 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  392 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0670
   chunk 17 optimal weight:    0.0870
   chunk 36 optimal weight:    5.9990
   chunk 69 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.4896

-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.070815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.049617 restraints weight = 25790.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 4.49
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.1191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6834  Z= 0.107
  Angle     :  0.560   8.091   9318  Z= 0.263
  Chirality :  0.044   0.291   1011
  Planarity :  0.003   0.035   1179
  Dihedral  :  8.237  66.288   1148
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  6.59 %
    Favored  : 92.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.31), residues: 791
  helix:  1.70 (0.27), residues: 393
  sheet:  0.63 (0.79), residues: 44
  loop : -0.78 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 163 
 HIS   0.003   0.001   HIS D 535 
 PHE   0.007   0.001   PHE D 369 
 TYR   0.010   0.001   TYR A 453 
 ARG   0.002   0.000   ARG D 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00837 (    7)
  link_NAG-ASN         : angle       3.46934 (   21)
  link_ALPHA1-6        : bond        0.00544 (    1)
  link_ALPHA1-6        : angle       1.94139 (    3)
  link_BETA1-4         : bond        0.00472 (    5)
  link_BETA1-4         : angle       1.84311 (   15)
  link_ALPHA1-3        : bond        0.01240 (    1)
  link_ALPHA1-3        : angle       1.79553 (    3)
  hydrogen bonds       : bond        0.04605 (  284)
  hydrogen bonds       : angle       4.13091 (  810)
  SS BOND              : bond        0.00335 (    7)
  SS BOND              : angle       0.82291 (   14)
  covalent geometry    : bond        0.00217 ( 6813)
  covalent geometry    : angle       0.52833 ( 9262)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.784 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8313 (t0) cc_final: 0.8109 (t0)
REVERT: D  108 LEU cc_start: 0.9194 (mm) cc_final: 0.8934 (tp)
REVERT: D  270 MET cc_start: 0.8370 (tpt) cc_final: 0.8119 (tpp)
REVERT: D  531 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8708 (tm-30)
  outliers start: 6
  outliers final: 1
  residues processed: 41
  average time/residue: 0.1499
  time to fit residues: 9.6442
Evaluate side-chains
  36 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 30 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    0.3980
   chunk 6 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3431 r_free = 0.3431 target = 0.070103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.048820 restraints weight = 26146.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.2860 rms_B_bonded: 4.49
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6834  Z= 0.135
  Angle     :  0.569   8.531   9318  Z= 0.267
  Chirality :  0.045   0.294   1011
  Planarity :  0.003   0.035   1179
  Dihedral  :  7.364  59.222   1148
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  7.74 %
    Favored  : 91.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.90 (0.31), residues: 791
  helix:  1.80 (0.27), residues: 393
  sheet:  0.43 (0.79), residues: 44
  loop : -0.76 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 163 
 HIS   0.002   0.001   HIS D 535 
 PHE   0.008   0.001   PHE D 315 
 TYR   0.011   0.001   TYR A 453 
 ARG   0.002   0.000   ARG D 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00732 (    7)
  link_NAG-ASN         : angle       3.34475 (   21)
  link_ALPHA1-6        : bond        0.00585 (    1)
  link_ALPHA1-6        : angle       1.93544 (    3)
  link_BETA1-4         : bond        0.00443 (    5)
  link_BETA1-4         : angle       1.69927 (   15)
  link_ALPHA1-3        : bond        0.01144 (    1)
  link_ALPHA1-3        : angle       1.94884 (    3)
  hydrogen bonds       : bond        0.04498 (  284)
  hydrogen bonds       : angle       4.04976 (  810)
  SS BOND              : bond        0.00298 (    7)
  SS BOND              : angle       0.77772 (   14)
  covalent geometry    : bond        0.00299 ( 6813)
  covalent geometry    : angle       0.54049 ( 9262)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
REVERT: A  467 ASP cc_start: 0.8502 (t0) cc_final: 0.8265 (t0)
REVERT: D   75 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8815 (mt-10)
REVERT: D  108 LEU cc_start: 0.9182 (mm) cc_final: 0.8902 (tp)
REVERT: D  270 MET cc_start: 0.8411 (tpt) cc_final: 0.8141 (tpp)
REVERT: D  531 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8759 (tm-30)
  outliers start: 7
  outliers final: 2
  residues processed: 39
  average time/residue: 0.1428
  time to fit residues: 8.7335
Evaluate side-chains
  37 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain D residue   75 GLU
Chi-restraints excluded: chain D residue  579 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0070
   chunk 45 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.9200

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

Flipped N/Q/H residues before XYZ refinement:
D  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.070163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.048817 restraints weight = 25904.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 4.49
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.1556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6834  Z= 0.132
  Angle     :  0.566   9.176   9318  Z= 0.266
  Chirality :  0.045   0.298   1011
  Planarity :  0.003   0.036   1179
  Dihedral  :  6.732  57.660   1148
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.03 %
    Favored  : 89.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.92 (0.31), residues: 791
  helix:  1.83 (0.27), residues: 392
  sheet:  0.37 (0.80), residues: 44
  loop : -0.76 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 477 
 HIS   0.003   0.001   HIS D  34 
 PHE   0.009   0.001   PHE D 315 
 TYR   0.011   0.001   TYR A 453 
 ARG   0.002   0.000   ARG D 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00706 (    7)
  link_NAG-ASN         : angle       3.26990 (   21)
  link_ALPHA1-6        : bond        0.00714 (    1)
  link_ALPHA1-6        : angle       1.83724 (    3)
  link_BETA1-4         : bond        0.00457 (    5)
  link_BETA1-4         : angle       1.52349 (   15)
  link_ALPHA1-3        : bond        0.01191 (    1)
  link_ALPHA1-3        : angle       1.89323 (    3)
  hydrogen bonds       : bond        0.04370 (  284)
  hydrogen bonds       : angle       4.02940 (  810)
  SS BOND              : bond        0.00294 (    7)
  SS BOND              : angle       0.76955 (   14)
  covalent geometry    : bond        0.00291 ( 6813)
  covalent geometry    : angle       0.53966 ( 9262)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  467 ASP cc_start: 0.8507 (t0) cc_final: 0.8281 (t0)
REVERT: D   75 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8782 (mt-10)
REVERT: D  108 LEU cc_start: 0.9167 (mm) cc_final: 0.8918 (tp)
REVERT: D  270 MET cc_start: 0.8426 (tpt) cc_final: 0.8157 (tpp)
REVERT: D  531 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8796 (tm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 42
  average time/residue: 0.1459
  time to fit residues: 9.5996
Evaluate side-chains
  40 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   75 GLU
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain D residue  579 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0040
   chunk 47 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 71 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 38 optimal weight:    0.2980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.070929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.049583 restraints weight = 26019.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 4.59
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6834  Z= 0.106
  Angle     :  0.557   9.644   9318  Z= 0.259
  Chirality :  0.044   0.290   1011
  Planarity :  0.003   0.036   1179
  Dihedral  :  6.273  57.742   1148
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  8.88 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.31), residues: 791
  helix:  1.89 (0.27), residues: 391
  sheet:  0.63 (0.82), residues: 42
  loop : -0.73 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 163 
 HIS   0.002   0.001   HIS D 535 
 PHE   0.008   0.001   PHE D 315 
 TYR   0.010   0.001   TYR D  50 
 ARG   0.002   0.000   ARG D 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00725 (    7)
  link_NAG-ASN         : angle       3.15611 (   21)
  link_ALPHA1-6        : bond        0.00818 (    1)
  link_ALPHA1-6        : angle       1.68354 (    3)
  link_BETA1-4         : bond        0.00469 (    5)
  link_BETA1-4         : angle       1.43975 (   15)
  link_ALPHA1-3        : bond        0.01202 (    1)
  link_ALPHA1-3        : angle       1.83031 (    3)
  hydrogen bonds       : bond        0.04029 (  284)
  hydrogen bonds       : angle       3.90226 (  810)
  SS BOND              : bond        0.00287 (    7)
  SS BOND              : angle       0.71652 (   14)
  covalent geometry    : bond        0.00227 ( 6813)
  covalent geometry    : angle       0.53239 ( 9262)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  467 ASP cc_start: 0.8533 (t0) cc_final: 0.8301 (t0)
REVERT: D  133 CYS cc_start: 0.6104 (OUTLIER) cc_final: 0.4680 (p)
REVERT: D  270 MET cc_start: 0.8491 (tpt) cc_final: 0.8095 (tpt)
REVERT: D  531 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8781 (tm-30)
  outliers start: 9
  outliers final: 4
  residues processed: 42
  average time/residue: 0.1385
  time to fit residues: 9.1390
Evaluate side-chains
  38 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue  133 CYS
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain D residue  579 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0970
   chunk 71 optimal weight:    4.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3416 r_free = 0.3416 target = 0.069865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.048424 restraints weight = 26268.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 4.60
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6834  Z= 0.150
  Angle     :  0.583   9.377   9318  Z= 0.274
  Chirality :  0.044   0.298   1011
  Planarity :  0.003   0.040   1179
  Dihedral  :  6.033  56.777   1148
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  8.88 %
    Favored  : 89.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.96 (0.31), residues: 791
  helix:  1.88 (0.28), residues: 390
  sheet:  0.30 (0.80), residues: 44
  loop : -0.74 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 163 
 HIS   0.003   0.001   HIS D 195 
 PHE   0.010   0.001   PHE D 315 
 TYR   0.012   0.001   TYR A 453 
 ARG   0.002   0.000   ARG D 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00653 (    7)
  link_NAG-ASN         : angle       3.15021 (   21)
  link_ALPHA1-6        : bond        0.00730 (    1)
  link_ALPHA1-6        : angle       1.66469 (    3)
  link_BETA1-4         : bond        0.00470 (    5)
  link_BETA1-4         : angle       1.44645 (   15)
  link_ALPHA1-3        : bond        0.01184 (    1)
  link_ALPHA1-3        : angle       1.92256 (    3)
  hydrogen bonds       : bond        0.04290 (  284)
  hydrogen bonds       : angle       3.99648 (  810)
  SS BOND              : bond        0.00293 (    7)
  SS BOND              : angle       0.79916 (   14)
  covalent geometry    : bond        0.00337 ( 6813)
  covalent geometry    : angle       0.55958 ( 9262)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  467 ASP cc_start: 0.8604 (t0) cc_final: 0.8404 (t0)
REVERT: D  133 CYS cc_start: 0.6213 (OUTLIER) cc_final: 0.4810 (p)
REVERT: D  248 LEU cc_start: 0.9724 (tp) cc_final: 0.9479 (tp)
REVERT: D  270 MET cc_start: 0.8443 (tpt) cc_final: 0.8168 (tpp)
REVERT: D  531 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8816 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 43
  average time/residue: 0.1529
  time to fit residues: 10.1407
Evaluate side-chains
  41 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue  133 CYS
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain D residue  579 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
D  42 GLN
** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.067953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.046628 restraints weight = 26533.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.2783 rms_B_bonded: 4.49
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   6834  Z= 0.269
  Angle     :  0.689  12.507   9318  Z= 0.329
  Chirality :  0.046   0.315   1011
  Planarity :  0.004   0.044   1179
  Dihedral  :  6.285  56.617   1148
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.31 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.74 (0.31), residues: 791
  helix:  1.74 (0.27), residues: 389
  sheet: -0.05 (0.76), residues: 49
  loop : -0.87 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 477 
 HIS   0.006   0.001   HIS D 195 
 PHE   0.014   0.002   PHE D 452 
 TYR   0.018   0.001   TYR A 453 
 ARG   0.003   0.000   ARG A 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00677 (    7)
  link_NAG-ASN         : angle       3.37370 (   21)
  link_ALPHA1-6        : bond        0.00523 (    1)
  link_ALPHA1-6        : angle       1.62001 (    3)
  link_BETA1-4         : bond        0.00511 (    5)
  link_BETA1-4         : angle       1.58574 (   15)
  link_ALPHA1-3        : bond        0.01173 (    1)
  link_ALPHA1-3        : angle       2.15134 (    3)
  hydrogen bonds       : bond        0.05251 (  284)
  hydrogen bonds       : angle       4.32265 (  810)
  SS BOND              : bond        0.00375 (    7)
  SS BOND              : angle       1.07866 (   14)
  covalent geometry    : bond        0.00611 ( 6813)
  covalent geometry    : angle       0.66573 ( 9262)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  133 CYS cc_start: 0.6128 (OUTLIER) cc_final: 0.4761 (p)
REVERT: D  248 LEU cc_start: 0.9718 (tp) cc_final: 0.9476 (tp)
REVERT: D  270 MET cc_start: 0.8583 (tpt) cc_final: 0.8257 (tpp)
REVERT: D  462 MET cc_start: 0.9356 (mmp) cc_final: 0.9124 (mtm)
  outliers start: 12
  outliers final: 5
  residues processed: 43
  average time/residue: 0.1338
  time to fit residues: 9.1014
Evaluate side-chains
  38 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue  133 CYS
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain D residue  579 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0040
   chunk 27 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 45 optimal weight:    0.1980
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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 = 0.3429 r_free = 0.3429 target = 0.070369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.048942 restraints weight = 26391.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 4.61
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6834  Z= 0.109
  Angle     :  0.588  10.620   9318  Z= 0.276
  Chirality :  0.044   0.317   1011
  Planarity :  0.003   0.047   1179
  Dihedral  :  5.886  59.128   1148
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.17 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.31), residues: 791
  helix:  1.88 (0.27), residues: 390
  sheet:  0.22 (0.80), residues: 44
  loop : -0.84 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 436 
 HIS   0.004   0.001   HIS D  34 
 PHE   0.011   0.001   PHE D 315 
 TYR   0.009   0.001   TYR D  50 
 ARG   0.002   0.000   ARG D 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00756 (    7)
  link_NAG-ASN         : angle       3.27466 (   21)
  link_ALPHA1-6        : bond        0.00746 (    1)
  link_ALPHA1-6        : angle       1.27846 (    3)
  link_BETA1-4         : bond        0.00532 (    5)
  link_BETA1-4         : angle       1.37245 (   15)
  link_ALPHA1-3        : bond        0.01099 (    1)
  link_ALPHA1-3        : angle       1.70257 (    3)
  hydrogen bonds       : bond        0.04157 (  284)
  hydrogen bonds       : angle       3.94693 (  810)
  SS BOND              : bond        0.00314 (    7)
  SS BOND              : angle       0.73584 (   14)
  covalent geometry    : bond        0.00230 ( 6813)
  covalent geometry    : angle       0.56377 ( 9262)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  133 CYS cc_start: 0.6152 (OUTLIER) cc_final: 0.4860 (p)
REVERT: D  248 LEU cc_start: 0.9724 (tp) cc_final: 0.9483 (tp)
REVERT: D  270 MET cc_start: 0.8466 (tpt) cc_final: 0.8150 (tpp)
REVERT: D  462 MET cc_start: 0.9370 (mmp) cc_final: 0.9123 (mtm)
REVERT: D  531 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8796 (tm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 40
  average time/residue: 0.1455
  time to fit residues: 9.2099
Evaluate side-chains
  38 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue  133 CYS
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  468 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 33 optimal weight:    8.9990
   chunk 45 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3424 r_free = 0.3424 target = 0.070138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.048732 restraints weight = 26691.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 4.61
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6834  Z= 0.125
  Angle     :  0.592   9.670   9318  Z= 0.278
  Chirality :  0.044   0.313   1011
  Planarity :  0.003   0.045   1179
  Dihedral  :  5.748  57.503   1148
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.03 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.92 (0.31), residues: 791
  helix:  1.92 (0.27), residues: 390
  sheet:  0.18 (0.79), residues: 44
  loop : -0.83 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 436 
 HIS   0.005   0.001   HIS D  34 
 PHE   0.009   0.001   PHE D 315 
 TYR   0.010   0.001   TYR D  50 
 ARG   0.002   0.000   ARG D 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00696 (    7)
  link_NAG-ASN         : angle       3.14685 (   21)
  link_ALPHA1-6        : bond        0.00627 (    1)
  link_ALPHA1-6        : angle       1.31904 (    3)
  link_BETA1-4         : bond        0.00525 (    5)
  link_BETA1-4         : angle       1.41844 (   15)
  link_ALPHA1-3        : bond        0.01038 (    1)
  link_ALPHA1-3        : angle       1.82063 (    3)
  hydrogen bonds       : bond        0.04109 (  284)
  hydrogen bonds       : angle       3.90288 (  810)
  SS BOND              : bond        0.00308 (    7)
  SS BOND              : angle       0.74704 (   14)
  covalent geometry    : bond        0.00277 ( 6813)
  covalent geometry    : angle       0.56948 ( 9262)

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

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

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1582 Ramachandran restraints generated.
    791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  133 CYS cc_start: 0.6088 (OUTLIER) cc_final: 0.4730 (p)
REVERT: D  248 LEU cc_start: 0.9729 (tp) cc_final: 0.9482 (tp)
REVERT: D  270 MET cc_start: 0.8668 (tpt) cc_final: 0.8240 (tpp)
REVERT: D  462 MET cc_start: 0.9344 (mmp) cc_final: 0.9065 (mtm)
REVERT: D  531 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8811 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 41
  average time/residue: 0.1473
  time to fit residues: 9.5454
Evaluate side-chains
  40 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue  133 CYS
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  468 ILE
Chi-restraints excluded: chain D residue  579 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    0.0770
   chunk 57 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 0 optimal weight:    0.6980
   chunk 75 optimal weight:    0.0980
   chunk 5 optimal weight:    0.0970
   chunk 23 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0670
   overall best weight:    0.2074

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

Flipped N/Q/H residues before XYZ refinement:
D  51 ASN
D 524 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.072352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.050996 restraints weight = 26196.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 4.65
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6834  Z= 0.097
  Angle     :  0.573   9.914   9318  Z= 0.267
  Chirality :  0.043   0.317   1011
  Planarity :  0.003   0.046   1179
  Dihedral  :  5.367  58.598   1148
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.03 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.30), residues: 791
  helix:  1.89 (0.27), residues: 392
  sheet:  0.51 (0.82), residues: 42
  loop : -0.74 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 436 
 HIS   0.003   0.000   HIS D  34 
 PHE   0.008   0.001   PHE D 315 
 TYR   0.008   0.001   TYR D  50 
 ARG   0.002   0.000   ARG D 177 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00786 (    7)
  link_NAG-ASN         : angle       3.07979 (   21)
  link_ALPHA1-6        : bond        0.00900 (    1)
  link_ALPHA1-6        : angle       1.25264 (    3)
  link_BETA1-4         : bond        0.00516 (    5)
  link_BETA1-4         : angle       1.30315 (   15)
  link_ALPHA1-3        : bond        0.00850 (    1)
  link_ALPHA1-3        : angle       1.49778 (    3)
  hydrogen bonds       : bond        0.03396 (  284)
  hydrogen bonds       : angle       3.75126 (  810)
  SS BOND              : bond        0.00322 (    7)
  SS BOND              : angle       0.76977 (   14)
  covalent geometry    : bond        0.00200 ( 6813)
  covalent geometry    : angle       0.55116 ( 9262)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2893.91 seconds
wall clock time: 51 minutes 3.63 seconds (3063.63 seconds total)