Starting phenix.real_space_refine
on Thu Jul  2 23:33:58 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8jyp_36729/07_2026/8jyp_36729.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jyp_36729/07_2026/8jyp_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_36729/07_2026/8jyp_36729.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jyp_36729/07_2026/8jyp_36729.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jyp_36729/07_2026/8jyp_36729.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jyp_36729/07_2026/8jyp_36729.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8jyp_36729/07_2026/8jyp_36729.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8jyp_36729/07_2026/8jyp_36729.cif"
  }
  resolution = 3.38
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 9
          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: 1.49, per 1000 atoms: 0.22
  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: 0.63
  Conformation dependent library (CDL) restraints added in 339.9 milliseconds
  

  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: 0.18
  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: 0.87

  Time building geometry restraints manager: 0.83 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: 3892
       21.77 -    43.54: 234
       43.54 -    65.31: 16
       65.31 -    87.08: 18
       87.08 -   108.85: 8
  Dihedral angle restraints: 4168
    sinusoidal: 1832
      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 4165 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:             3.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.260
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
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  : 14.736 108.849   2647
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (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
 ARG   0.001   0.000   ARG A 357 
 TYR   0.011   0.001   TYR A 453 
 PHE   0.016   0.001   PHE D  32 
 TRP   0.031   0.001   TRP D 163 
 HIS   0.003   0.001   HIS D  34 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.17 ( 6813)
  covalent geometry    : angle       0.62191 /  0.31 ( 9262)
  SS BOND              : bond        0.00326 /  0.22 (    7)
  SS BOND              : angle       0.78482 /  0.50 (   14)
  hydrogen bonds       : bond        0.16587 / 10.66 (  284)
  hydrogen bonds       : angle       6.03160 /  4.05 (  810)
  link_ALPHA1-3        : bond        0.00328 /  0.17 (    1)
  link_ALPHA1-3        : angle       1.52227 /  1.17 (    3)
  link_ALPHA1-6        : bond        0.00367 /  0.19 (    1)
  link_ALPHA1-6        : angle       1.63473 /  1.29 (    3)
  link_BETA1-4         : bond        0.00286 /  0.21 (    5)
  link_BETA1-4         : angle       1.86959 /  1.16 (   15)
  link_NAG-ASN         : bond        0.00921 /  0.53 (    7)
  link_NAG-ASN         : angle       3.83877 /  2.62 (   21)

*********************** 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  : 0.273 
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: 0.0582
  time to fit residues: 4.4152
Evaluate side-chains
  37 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 370 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.070680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.049604 restraints weight = 25718.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.2883 rms_B_bonded: 4.43
r_work: 0.2722 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.0850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6834  Z= 0.136
  Angle     :  0.589   7.671   9318  Z= 0.283
  Chirality :  0.045   0.293   1011
  Planarity :  0.003   0.035   1179
  Dihedral  : 10.545  77.707   1110
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  5.01 %
    Favored  : 94.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.30), residues: 791
  helix:  1.64 (0.27), residues: 391
  sheet:  0.88 (0.78), residues: 44
  loop : -0.86 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 177 
 TYR   0.011   0.001   TYR A 453 
 PHE   0.014   0.001   PHE D 315 
 TRP   0.020   0.001   TRP D 163 
 HIS   0.005   0.001   HIS D 535 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 6813)
  covalent geometry    : angle       0.55754 /  0.28 ( 9262)
  SS BOND              : bond        0.00317 /  0.23 (    7)
  SS BOND              : angle       0.78692 /  0.48 (   14)
  hydrogen bonds       : bond        0.05427 /  3.84 (  284)
  hydrogen bonds       : angle       4.46951 /  3.11 (  810)
  link_ALPHA1-3        : bond        0.00949 /  0.50 (    1)
  link_ALPHA1-3        : angle       2.35718 /  1.46 (    3)
  link_ALPHA1-6        : bond        0.00279 /  0.15 (    1)
  link_ALPHA1-6        : angle       2.35195 /  1.89 (    3)
  link_BETA1-4         : bond        0.00424 /  0.29 (    5)
  link_BETA1-4         : angle       1.95417 /  1.27 (   15)
  link_NAG-ASN         : bond        0.00859 /  0.49 (    7)
  link_NAG-ASN         : angle       3.46355 /  2.43 (   21)

*********************** 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
  42 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  467 ASP cc_start: 0.8527 (t0) cc_final: 0.8266 (t0)
REVERT: A  493 GLN cc_start: 0.9169 (tp40) cc_final: 0.8826 (tp-100)
REVERT: D  270 MET cc_start: 0.8571 (tpt) cc_final: 0.8190 (tpp)
REVERT: D  531 GLN cc_start: 0.9343 (tm-30) cc_final: 0.9019 (tm-30)
  outliers start: 5
  outliers final: 1
  residues processed: 40
  average time/residue: 0.0452
  time to fit residues: 2.9592
Evaluate side-chains
  35 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 56 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.068413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.047311 restraints weight = 26102.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.2814 rms_B_bonded: 4.40
r_work: 0.2648 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6834  Z= 0.240
  Angle     :  0.653  10.097   9318  Z= 0.314
  Chirality :  0.046   0.298   1011
  Planarity :  0.003   0.033   1179
  Dihedral  :  8.813  67.703   1110
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  7.59 %
    Favored  : 91.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.31), residues: 791
  helix:  1.66 (0.27), residues: 392
  sheet:  0.48 (0.76), residues: 48
  loop : -0.91 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 177 
 TYR   0.019   0.001   TYR A 453 
 PHE   0.012   0.001   PHE D 315 
 TRP   0.014   0.001   TRP D 163 
 HIS   0.004   0.001   HIS D 373 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00544 /  0.24 ( 6813)
  covalent geometry    : angle       0.62474 /  0.31 ( 9262)
  SS BOND              : bond        0.00349 /  0.24 (    7)
  SS BOND              : angle       1.00415 /  0.63 (   14)
  hydrogen bonds       : bond        0.05564 /  3.90 (  284)
  hydrogen bonds       : angle       4.44523 /  3.10 (  810)
  link_ALPHA1-3        : bond        0.01046 /  0.55 (    1)
  link_ALPHA1-3        : angle       2.16048 /  1.34 (    3)
  link_ALPHA1-6        : bond        0.00362 /  0.19 (    1)
  link_ALPHA1-6        : angle       2.18805 /  1.72 (    3)
  link_BETA1-4         : bond        0.00442 /  0.32 (    5)
  link_BETA1-4         : angle       1.92751 /  1.27 (   15)
  link_NAG-ASN         : bond        0.00755 /  0.43 (    7)
  link_NAG-ASN         : angle       3.54616 /  2.40 (   21)

*********************** 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
  40 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  493 GLN cc_start: 0.9161 (tp40) cc_final: 0.8909 (tp-100)
REVERT: D  270 MET cc_start: 0.8628 (tpt) cc_final: 0.8306 (tpp)
REVERT: D  531 GLN cc_start: 0.9405 (tm-30) cc_final: 0.9084 (tm-30)
  outliers start: 5
  outliers final: 2
  residues processed: 39
  average time/residue: 0.0525
  time to fit residues: 3.3240
Evaluate side-chains
  35 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain D residue  506 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 43 optimal weight:    0.1980
   chunk 5 optimal weight:    0.0370
   chunk 36 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 28 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.5458

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.070165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.048993 restraints weight = 25877.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 4.45
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6834  Z= 0.110
  Angle     :  0.564   9.182   9318  Z= 0.264
  Chirality :  0.044   0.298   1011
  Planarity :  0.003   0.035   1179
  Dihedral  :  7.567  59.536   1110
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  8.45 %
    Favored  : 90.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.31), residues: 791
  helix:  1.80 (0.27), residues: 393
  sheet:  0.36 (0.79), residues: 44
  loop : -0.85 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 177 
 TYR   0.010   0.001   TYR A 453 
 PHE   0.010   0.001   PHE D 315 
 TRP   0.013   0.001   TRP D 163 
 HIS   0.002   0.001   HIS D 535 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.11 ( 6813)
  covalent geometry    : angle       0.53393 /  0.26 ( 9262)
  SS BOND              : bond        0.00325 /  0.23 (    7)
  SS BOND              : angle       0.78132 /  0.51 (   14)
  hydrogen bonds       : bond        0.04457 /  3.16 (  284)
  hydrogen bonds       : angle       4.08736 /  2.85 (  810)
  link_ALPHA1-3        : bond        0.01228 /  0.65 (    1)
  link_ALPHA1-3        : angle       1.94263 /  1.25 (    3)
  link_ALPHA1-6        : bond        0.00594 /  0.31 (    1)
  link_ALPHA1-6        : angle       1.84191 /  1.47 (    3)
  link_BETA1-4         : bond        0.00439 /  0.34 (    5)
  link_BETA1-4         : angle       1.66463 /  1.11 (   15)
  link_NAG-ASN         : bond        0.00813 /  0.51 (    7)
  link_NAG-ASN         : angle       3.44011 /  2.34 (   21)

*********************** 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
  41 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: D   75 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8832 (mt-10)
REVERT: D  270 MET cc_start: 0.8398 (tpt) cc_final: 0.8099 (tpp)
REVERT: D  531 GLN cc_start: 0.9159 (tm-30) cc_final: 0.8778 (tm-30)
  outliers start: 5
  outliers final: 3
  residues processed: 40
  average time/residue: 0.0550
  time to fit residues: 3.4485
Evaluate side-chains
  36 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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   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 9 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0050
   chunk 48 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0000
   overall best weight:    0.7202

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.070327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.048992 restraints weight = 26218.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 4.52
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6834  Z= 0.118
  Angle     :  0.561   8.945   9318  Z= 0.263
  Chirality :  0.045   0.300   1011
  Planarity :  0.003   0.035   1179
  Dihedral  :  6.916  57.740   1110
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.45 %
    Favored  : 90.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.31), residues: 791
  helix:  1.78 (0.27), residues: 393
  sheet:  0.52 (0.81), residues: 42
  loop : -0.79 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 177 
 TYR   0.010   0.001   TYR A 453 
 PHE   0.010   0.001   PHE D 315 
 TRP   0.010   0.001   TRP D 163 
 HIS   0.002   0.001   HIS D 535 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.12 ( 6813)
  covalent geometry    : angle       0.53387 /  0.26 ( 9262)
  SS BOND              : bond        0.00298 /  0.21 (    7)
  SS BOND              : angle       0.77383 /  0.50 (   14)
  hydrogen bonds       : bond        0.04293 /  3.06 (  284)
  hydrogen bonds       : angle       4.00840 /  2.79 (  810)
  link_ALPHA1-3        : bond        0.01133 /  0.60 (    1)
  link_ALPHA1-3        : angle       1.94690 /  1.23 (    3)
  link_ALPHA1-6        : bond        0.00682 /  0.36 (    1)
  link_ALPHA1-6        : angle       1.78741 /  1.38 (    3)
  link_BETA1-4         : bond        0.00471 /  0.36 (    5)
  link_BETA1-4         : angle       1.55159 /  1.03 (   15)
  link_NAG-ASN         : bond        0.00721 /  0.46 (    7)
  link_NAG-ASN         : angle       3.28691 /  2.22 (   21)

*********************** 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: 10
    poor density    : 34
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   75 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8801 (mt-10)
REVERT: D  270 MET cc_start: 0.8423 (tpt) cc_final: 0.8162 (tpp)
REVERT: D  531 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8797 (tm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 42
  average time/residue: 0.0491
  time to fit residues: 3.2517
Evaluate side-chains
  39 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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 8 optimal weight:    0.5980
   chunk 15 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.069348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.048074 restraints weight = 26670.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.2828 rms_B_bonded: 4.55
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6834  Z= 0.163
  Angle     :  0.594   9.777   9318  Z= 0.280
  Chirality :  0.045   0.306   1011
  Planarity :  0.003   0.034   1179
  Dihedral  :  6.537  57.190   1110
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.46 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.31), residues: 791
  helix:  1.82 (0.27), residues: 391
  sheet:  0.40 (0.79), residues: 43
  loop : -0.85 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 177 
 TYR   0.013   0.001   TYR A 453 
 PHE   0.010   0.001   PHE D 315 
 TRP   0.011   0.001   TRP D 477 
 HIS   0.003   0.001   HIS D  34 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 ( 6813)
  covalent geometry    : angle       0.56953 /  0.27 ( 9262)
  SS BOND              : bond        0.00308 /  0.20 (    7)
  SS BOND              : angle       0.83423 /  0.53 (   14)
  hydrogen bonds       : bond        0.04551 /  3.23 (  284)
  hydrogen bonds       : angle       4.06240 /  2.82 (  810)
  link_ALPHA1-3        : bond        0.01159 /  0.61 (    1)
  link_ALPHA1-3        : angle       2.03392 /  1.23 (    3)
  link_ALPHA1-6        : bond        0.00703 /  0.37 (    1)
  link_ALPHA1-6        : angle       1.75839 /  1.30 (    3)
  link_BETA1-4         : bond        0.00458 /  0.37 (    5)
  link_BETA1-4         : angle       1.50202 /  0.99 (   15)
  link_NAG-ASN         : bond        0.00689 /  0.43 (    7)
  link_NAG-ASN         : angle       3.26034 /  2.18 (   21)

*********************** 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: 10
    poor density    : 34
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  133 CYS cc_start: 0.5987 (OUTLIER) cc_final: 0.4574 (p)
REVERT: D  270 MET cc_start: 0.8449 (tpt) cc_final: 0.8180 (tpp)
REVERT: D  462 MET cc_start: 0.9292 (mmp) cc_final: 0.9076 (mtm)
REVERT: D  531 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8835 (tm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 41
  average time/residue: 0.0571
  time to fit residues: 3.7023
Evaluate side-chains
  39 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0980
   chunk 71 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.070449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.049068 restraints weight = 26112.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 4.59
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6834  Z= 0.114
  Angle     :  0.566   9.451   9318  Z= 0.265
  Chirality :  0.044   0.307   1011
  Planarity :  0.003   0.041   1179
  Dihedral  :  6.087  57.908   1110
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.60 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.31), residues: 791
  helix:  1.87 (0.27), residues: 390
  sheet:  0.54 (0.82), residues: 42
  loop : -0.76 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 177 
 TYR   0.010   0.001   TYR A 453 
 PHE   0.008   0.001   PHE D 315 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.002   0.001   HIS D 373 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 6813)
  covalent geometry    : angle       0.54102 /  0.26 ( 9262)
  SS BOND              : bond        0.00294 /  0.20 (    7)
  SS BOND              : angle       0.74963 /  0.49 (   14)
  hydrogen bonds       : bond        0.04100 /  2.92 (  284)
  hydrogen bonds       : angle       3.93152 /  2.73 (  810)
  link_ALPHA1-3        : bond        0.01125 /  0.59 (    1)
  link_ALPHA1-3        : angle       1.81909 /  1.14 (    3)
  link_ALPHA1-6        : bond        0.00753 /  0.40 (    1)
  link_ALPHA1-6        : angle       1.52233 /  1.18 (    3)
  link_BETA1-4         : bond        0.00448 /  0.35 (    5)
  link_BETA1-4         : angle       1.39705 /  0.92 (   15)
  link_NAG-ASN         : bond        0.00706 /  0.47 (    7)
  link_NAG-ASN         : angle       3.21513 /  2.15 (   21)

*********************** 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
  44 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  133 CYS cc_start: 0.5935 (OUTLIER) cc_final: 0.4553 (p)
REVERT: D  248 LEU cc_start: 0.9720 (tp) cc_final: 0.9470 (tp)
REVERT: D  270 MET cc_start: 0.8514 (tpt) cc_final: 0.8204 (tpp)
REVERT: D  462 MET cc_start: 0.9278 (mmp) cc_final: 0.9052 (mtm)
REVERT: D  531 GLN cc_start: 0.9213 (tm-30) cc_final: 0.8816 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 43
  average time/residue: 0.0569
  time to fit residues: 3.9149
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  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  434 ILE
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 29 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0670
   chunk 76 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0770
   chunk 13 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.4476

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.071375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.049957 restraints weight = 26375.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 4.64
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1919

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= 0.100
  Angle     :  0.558   9.143   9318  Z= 0.261
  Chirality :  0.043   0.294   1011
  Planarity :  0.003   0.044   1179
  Dihedral  :  5.639  57.444   1110
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  9.60 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.03 (0.31), residues: 791
  helix:  1.91 (0.27), residues: 391
  sheet:  0.55 (0.83), residues: 42
  loop : -0.71 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 177 
 TYR   0.009   0.001   TYR D  50 
 PHE   0.007   0.001   PHE D 504 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.002   0.000   HIS D 535 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00212 /  0.10 ( 6813)
  covalent geometry    : angle       0.53544 /  0.26 ( 9262)
  SS BOND              : bond        0.00294 /  0.20 (    7)
  SS BOND              : angle       0.73274 /  0.48 (   14)
  hydrogen bonds       : bond        0.03714 /  2.65 (  284)
  hydrogen bonds       : angle       3.83193 /  2.65 (  810)
  link_ALPHA1-3        : bond        0.00978 /  0.51 (    1)
  link_ALPHA1-3        : angle       1.68881 /  1.07 (    3)
  link_ALPHA1-6        : bond        0.00822 /  0.43 (    1)
  link_ALPHA1-6        : angle       1.31586 /  1.12 (    3)
  link_BETA1-4         : bond        0.00536 /  0.45 (    5)
  link_BETA1-4         : angle       1.35504 /  0.90 (   15)
  link_NAG-ASN         : bond        0.00711 /  0.47 (    7)
  link_NAG-ASN         : angle       3.05342 /  2.06 (   21)

*********************** 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: 11
    poor density    : 34
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  133 CYS cc_start: 0.5925 (OUTLIER) cc_final: 0.4508 (p)
REVERT: D  248 LEU cc_start: 0.9724 (tp) cc_final: 0.9477 (tp)
REVERT: D  270 MET cc_start: 0.8490 (tpt) cc_final: 0.8196 (tpp)
REVERT: D  462 MET cc_start: 0.9314 (mmp) cc_final: 0.8978 (mpp)
REVERT: D  531 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8785 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 44
  average time/residue: 0.0582
  time to fit residues: 4.0748
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  : 0.231 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 61 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 66 optimal weight:    9.9990
   chunk 59 optimal weight:    0.0670
   chunk 51 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.6318

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.071042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.049665 restraints weight = 26429.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 4.63
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6834  Z= 0.112
  Angle     :  0.575   9.272   9318  Z= 0.267
  Chirality :  0.043   0.303   1011
  Planarity :  0.003   0.044   1179
  Dihedral  :  5.505  56.985   1110
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.31), residues: 791
  helix:  1.90 (0.27), residues: 392
  sheet:  0.62 (0.83), residues: 42
  loop : -0.68 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 177 
 TYR   0.010   0.001   TYR D  50 
 PHE   0.012   0.001   PHE A 392 
 TRP   0.009   0.001   TRP D 477 
 HIS   0.004   0.001   HIS D  34 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 6813)
  covalent geometry    : angle       0.55264 /  0.26 ( 9262)
  SS BOND              : bond        0.00295 /  0.21 (    7)
  SS BOND              : angle       0.74843 /  0.48 (   14)
  hydrogen bonds       : bond        0.03769 /  2.68 (  284)
  hydrogen bonds       : angle       3.85314 /  2.67 (  810)
  link_ALPHA1-3        : bond        0.01033 /  0.54 (    1)
  link_ALPHA1-3        : angle       1.86928 /  1.17 (    3)
  link_ALPHA1-6        : bond        0.00715 /  0.38 (    1)
  link_ALPHA1-6        : angle       1.29753 /  1.13 (    3)
  link_BETA1-4         : bond        0.00537 /  0.44 (    5)
  link_BETA1-4         : angle       1.37191 /  0.91 (   15)
  link_NAG-ASN         : bond        0.00684 /  0.46 (    7)
  link_NAG-ASN         : angle       3.05992 /  2.04 (   21)

*********************** 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
  42 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  133 CYS cc_start: 0.6047 (OUTLIER) cc_final: 0.4732 (p)
REVERT: D  248 LEU cc_start: 0.9729 (tp) cc_final: 0.9505 (tp)
REVERT: D  270 MET cc_start: 0.8482 (tpt) cc_final: 0.8199 (tpp)
REVERT: D  531 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8787 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 41
  average time/residue: 0.0558
  time to fit residues: 3.4827
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  : 0.148 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0370
   chunk 56 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.6258

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  42 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.071330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.049857 restraints weight = 26235.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 4.63
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2061

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= 0.110
  Angle     :  0.577   9.605   9318  Z= 0.268
  Chirality :  0.043   0.305   1011
  Planarity :  0.003   0.044   1179
  Dihedral  :  5.395  56.860   1110
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.89 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.31), residues: 791
  helix:  1.90 (0.27), residues: 392
  sheet:  0.70 (0.83), residues: 42
  loop : -0.66 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 177 
 TYR   0.009   0.001   TYR D  50 
 PHE   0.011   0.001   PHE A 392 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.003   0.001   HIS D  34 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00243 /  0.11 ( 6813)
  covalent geometry    : angle       0.55534 /  0.26 ( 9262)
  SS BOND              : bond        0.00293 /  0.20 (    7)
  SS BOND              : angle       0.72764 /  0.48 (   14)
  hydrogen bonds       : bond        0.03747 /  2.66 (  284)
  hydrogen bonds       : angle       3.84329 /  2.66 (  810)
  link_ALPHA1-3        : bond        0.00960 /  0.51 (    1)
  link_ALPHA1-3        : angle       1.74506 /  1.10 (    3)
  link_ALPHA1-6        : bond        0.00704 /  0.37 (    1)
  link_ALPHA1-6        : angle       1.24972 /  1.10 (    3)
  link_BETA1-4         : bond        0.00497 /  0.40 (    5)
  link_BETA1-4         : angle       1.35647 /  0.90 (   15)
  link_NAG-ASN         : bond        0.00681 /  0.46 (    7)
  link_NAG-ASN         : angle       3.02582 /  2.03 (   21)

********************** 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  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  133 CYS cc_start: 0.6104 (OUTLIER) cc_final: 0.4786 (p)
REVERT: D  248 LEU cc_start: 0.9726 (tp) cc_final: 0.9495 (tp)
REVERT: D  270 MET cc_start: 0.8463 (tpt) cc_final: 0.8191 (tpp)
REVERT: D  462 MET cc_start: 0.9328 (mmp) cc_final: 0.9000 (mpp)
REVERT: D  531 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8745 (tm-30)
  outliers start: 8
  outliers final: 6
  residues processed: 41
  average time/residue: 0.0537
  time to fit residues: 3.5093
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  : 0.201 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 74 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 14 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9990
   chunk 43 optimal weight:    0.1980
   chunk 61 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 69 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.5580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.071436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.050035 restraints weight = 26182.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 4.62
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6834  Z= 0.104
  Angle     :  0.577   9.408   9318  Z= 0.266
  Chirality :  0.043   0.304   1011
  Planarity :  0.003   0.044   1179
  Dihedral  :  5.333  56.852   1110
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.74 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.31), residues: 791
  helix:  1.92 (0.27), residues: 392
  sheet:  0.74 (0.83), residues: 42
  loop : -0.66 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 177 
 TYR   0.010   0.001   TYR D  50 
 PHE   0.011   0.001   PHE A 392 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.005   0.001   HIS D  34 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.10 ( 6813)
  covalent geometry    : angle       0.55607 /  0.26 ( 9262)
  SS BOND              : bond        0.00296 /  0.20 (    7)
  SS BOND              : angle       0.73153 /  0.48 (   14)
  hydrogen bonds       : bond        0.03661 /  2.61 (  284)
  hydrogen bonds       : angle       3.78597 /  2.62 (  810)
  link_ALPHA1-3        : bond        0.00912 /  0.48 (    1)
  link_ALPHA1-3        : angle       1.72220 /  1.10 (    3)
  link_ALPHA1-6        : bond        0.00703 /  0.37 (    1)
  link_ALPHA1-6        : angle       1.25008 /  1.09 (    3)
  link_BETA1-4         : bond        0.00504 /  0.41 (    5)
  link_BETA1-4         : angle       1.35697 /  0.90 (   15)
  link_NAG-ASN         : bond        0.00680 /  0.46 (    7)
  link_NAG-ASN         : angle       3.00803 /  2.02 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1414.01 seconds
wall clock time: 25 minutes 1.40 seconds (1501.40 seconds total)