Starting phenix.real_space_refine
on Sat May 10 10:56:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c6o_45253/05_2025/9c6o_45253.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c6o_45253/05_2025/9c6o_45253.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c6o_45253/05_2025/9c6o_45253.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c6o_45253/05_2025/9c6o_45253.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c6o_45253/05_2025/9c6o_45253.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c6o_45253/05_2025/9c6o_45253.cif"
  }
  resolution = 2.77
  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=   0.069
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    3925      2.51       5
     N    1029      2.21       5
     O    1098      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 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: 6086
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1350
          Classifications: {'peptide': 195}
          Incomplete info: {'truncation_to_alanine': 64}
          Link IDs: {'PTRANS': 15, 'TRANS': 179}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 186
          Unresolved non-hydrogen angles: 242
          Unresolved non-hydrogen dihedrals: 145
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 94
    Chain: "A"
      Number of atoms: 4571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 582, 4571
          Classifications: {'peptide': 582}
          Incomplete info: {'truncation_to_alanine': 89}
          Link IDs: {'PTRANS': 23, 'TRANS': 558}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 263
          Unresolved non-hydrogen angles: 332
          Unresolved non-hydrogen dihedrals: 196
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 18, 'ASN:plan1': 9, 'HIS:plan': 1, 'GLU:plan': 18, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 183
    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: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 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: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 4.33, per 1000 atoms: 0.71
  Number of scatterers: 6086
  At special positions: 0
  Unit cell: (89, 94, 105, 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      34     16.00
     O    1098      8.00
     N    1029      7.00
     C    3925      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 425 " - pdb=" SG  CYS B 478 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 503 " - pdb=" SG  CYS B 538 " distance=2.09
    Simple disulfide: pdb=" SG  CYS B 506 " - pdb=" SG  CYS B 520 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 342 " - pdb=" SG  CYS A 359 " distance=2.12
    Simple disulfide: pdb=" SG  CYS A 528 " - pdb=" SG  CYS A 540 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A 801 " - " ASN A 297 "
      " NAG A 802 " - " ASN A  76 "
      " NAG A 803 " - " ASN A  85 "
      " NAG A 804 " - " ASN A 320 "
      " NAG A 805 " - " ASN A 327 "
      " NAG A 806 " - " ASN A 544 "
      " NAG B 700 " - " ASN B 550 "
      " NAG C   1 " - " ASN B 496 "
      " NAG D   1 " - " ASN A  54 "
  Time building additional restraints: 1.46
  Conformation dependent library (CDL) restraints added in 828.9 milliseconds
  

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1474

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 5 sheets defined
      58.2% alpha, 10.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'B' and resid 386 through 390
    Processing helix  chain 'B' and resid 395 through 399
      removed outlier: 3.795A  pdb=" N   PHE B 399 " --> pdb=" O   PRO B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 415
    Processing helix  chain 'B' and resid 452 through 457
    Processing helix  chain 'B' and resid 463 through 468
    Processing helix  chain 'B' and resid 535 through 549
      removed outlier: 4.782A  pdb=" N   VAL B 541 " --> pdb=" O   SER B 537 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE B 547 " --> pdb=" O   LEU B 543 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   GLY B 549 " --> pdb=" O   GLY B 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 22 through 53
      removed outlier: 3.888A  pdb=" N   LYS A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 82
      removed outlier: 3.523A  pdb=" N   ILE A  80 " --> pdb=" O   ASN A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 84
      No H-bonds generated for 'chain 'A' and resid 83 through 84'
    Processing helix  chain 'A' and resid 85 through 89
    Processing helix  chain 'A' and resid 91 through 103
    Processing helix  chain 'A' and resid 111 through 127
    Processing helix  chain 'A' and resid 145 through 153
    Processing helix  chain 'A' and resid 155 through 170
    Processing helix  chain 'A' and resid 174 through 192
    Processing helix  chain 'A' and resid 196 through 202
    Processing helix  chain 'A' and resid 203 through 206
    Processing helix  chain 'A' and resid 210 through 214
      removed outlier: 4.163A  pdb=" N   ALA A 214 " --> pdb=" O   GLU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 250
      removed outlier: 3.660A  pdb=" N   ASP A 222 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU A 230 " --> pdb=" O   ARG A 226 " (cutoff:3.500A)
      Proline residue:  A 233  - end of helix
      removed outlier: 3.662A  pdb=" N   ASP A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 265
      No H-bonds generated for 'chain 'A' and resid 263 through 265'
    Processing helix  chain 'A' and resid 273 through 275
      No H-bonds generated for 'chain 'A' and resid 273 through 275'
    Processing helix  chain 'A' and resid 276 through 281
    Processing helix  chain 'A' and resid 291 through 298
    Processing helix  chain 'A' and resid 301 through 317
    Processing helix  chain 'A' and resid 324 through 329
    Processing helix  chain 'A' and resid 364 through 383
      removed outlier: 3.732A  pdb=" N   HIS A 371 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 391
    Processing helix  chain 'A' and resid 397 through 410
      removed outlier: 3.545A  pdb=" N   GLY A 403 " --> pdb=" O   HIS A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 419
    Processing helix  chain 'A' and resid 430 through 445
    Processing helix  chain 'A' and resid 447 through 464
    Processing helix  chain 'A' and resid 467 through 469
      No H-bonds generated for 'chain 'A' and resid 467 through 469'
    Processing helix  chain 'A' and resid 470 through 483
    Processing helix  chain 'A' and resid 497 through 500
    Processing helix  chain 'A' and resid 501 through 506
    Processing helix  chain 'A' and resid 511 through 531
    Processing helix  chain 'A' and resid 536 through 540
    Processing helix  chain 'A' and resid 545 through 557
      removed outlier: 3.760A  pdb=" N   MET A 555 " --> pdb=" O   LYS A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 573
      removed outlier: 3.721A  pdb=" N   ILE A 571 " --> pdb=" O   ALA A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 586
    Processing helix  chain 'A' and resid 586 through 597
    Processing sheet with id=AA1, first strand: chain 'B' and resid 400 through 404
      removed outlier: 6.682A  pdb=" N   TYR B 483 " --> pdb=" O   VAL B 420 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   VAL B 420 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 518 through 525
      removed outlier: 4.436A  pdb=" N   GLY B 505 " --> pdb=" O   ILE B 521 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   GLU B 523 " --> pdb=" O   CYS B 503 " (cutoff:3.500A)
      removed outlier: 9.680A  pdb=" N   CYS B 503 " --> pdb=" O   GLU B 523 " (cutoff:3.500A)
      removed outlier: 10.583A  pdb=" N   VAL B 525 " --> pdb=" O   THR B 501 " (cutoff:3.500A)
      removed outlier: 12.818A  pdb=" N   THR B 501 " --> pdb=" O   VAL B 525 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL B 574 " --> pdb=" O   THR B 501 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   CYS B 503 " --> pdb=" O   LYS B 572 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LYS B 572 " --> pdb=" O   CYS B 503 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132
      removed outlier: 6.024A  pdb=" N   GLN A 138 " --> pdb=" O   LYS A 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 260 through 261
      removed outlier: 6.188A  pdb=" N   LEU A 260 " --> pdb=" O   VAL A 486 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 348

    332 hydrogen bonds defined for protein.
    930 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: 1.85

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 974
        1.30 -     1.43: 1738
        1.43 -     1.57: 3473
        1.57 -     1.70: 9
        1.70 -     1.83: 54
  Bond restraints: 6248
  Sorted by residual:
  bond pdb=" C   LYS A  93 "
       pdb=" O   LYS A  93 "
    ideal  model  delta    sigma   weight residual
    1.237  1.170  0.067 1.19e-02 7.06e+03 3.18e+01
  bond pdb=" N   ILE B 547 "
       pdb=" CA  ILE B 547 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 8.60e-03 1.35e+04 1.75e+01
  bond pdb=" NE  ARG A 338 "
       pdb=" CZ  ARG A 338 "
    ideal  model  delta    sigma   weight residual
    1.326  1.370 -0.044 1.10e-02 8.26e+03 1.60e+01
  bond pdb=" N   ARG A 587 "
       pdb=" CA  ARG A 587 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.04e-02 9.25e+03 1.38e+01
  bond pdb=" N   VAL B 528 "
       pdb=" CA  VAL B 528 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.22e-02 6.72e+03 9.78e+00
  ... (remaining 6243 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 7578
        1.74 -     3.48: 773
        3.48 -     5.22: 90
        5.22 -     6.96: 55
        6.96 -     8.70: 13
  Bond angle restraints: 8509
  Sorted by residual:
  angle pdb=" C   ASN A 135 "
        pdb=" N   PRO A 136 "
        pdb=" CA  PRO A 136 "
      ideal   model   delta    sigma   weight residual
     119.82  128.11   -8.29 9.80e-01 1.04e+00 7.15e+01
  angle pdb=" C   VAL A 281 "
        pdb=" N   PRO A 282 "
        pdb=" CA  PRO A 282 "
      ideal   model   delta    sigma   weight residual
     119.24  127.94   -8.70 1.04e+00 9.25e-01 7.00e+01
  angle pdb=" C   ASN B 513 "
        pdb=" N   PRO B 514 "
        pdb=" CA  PRO B 514 "
      ideal   model   delta    sigma   weight residual
     119.82  127.52   -7.70 9.80e-01 1.04e+00 6.17e+01
  angle pdb=" C   LYS A 132 "
        pdb=" N   PRO A 133 "
        pdb=" CA  PRO A 133 "
      ideal   model   delta    sigma   weight residual
     119.56  127.20   -7.64 1.01e+00 9.80e-01 5.73e+01
  angle pdb=" C   SER A 255 "
        pdb=" N   PRO A 256 "
        pdb=" CA  PRO A 256 "
      ideal   model   delta    sigma   weight residual
     119.56  126.69   -7.13 1.02e+00 9.61e-01 4.88e+01
  ... (remaining 8504 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.29: 3683
       21.29 -    42.59: 111
       42.59 -    63.88: 22
       63.88 -    85.17: 13
       85.17 -   106.47: 5
  Dihedral angle restraints: 3834
    sinusoidal: 1554
      harmonic: 2280
  Sorted by residual:
  dihedral pdb=" O4  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -177.76  106.47     1      3.00e+01 1.11e-03 1.37e+01
  dihedral pdb=" C3  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -58.27  105.89     1      3.00e+01 1.11e-03 1.36e+01
  dihedral pdb=" C6  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O4  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -163.34  -63.10 -100.24     1      3.00e+01 1.11e-03 1.26e+01
  ... (remaining 3831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.171: 898
       0.171 -    0.342: 49
       0.342 -    0.512: 3
       0.512 -    0.683: 0
       0.683 -    0.854: 1
  Chirality restraints: 951
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.54    0.14 2.00e-02 2.50e+03 4.93e+01
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.49    0.09 2.00e-02 2.50e+03 2.19e+01
  chirality pdb=" C1  NAG A 804 "
            pdb=" ND2 ASN A 320 "
            pdb=" C2  NAG A 804 "
            pdb=" O5  NAG A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.55   -0.85 2.00e-01 2.50e+01 1.82e+01
  ... (remaining 948 not shown)

  Planarity restraints: 1087
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 806 "    0.115 2.00e-02 2.50e+03   9.78e-02 1.20e+02
        pdb=" C7  NAG A 806 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8  NAG A 806 "   -0.027 2.00e-02 2.50e+03
        pdb=" N2  NAG A 806 "   -0.157 2.00e-02 2.50e+03
        pdb=" O7  NAG A 806 "    0.093 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 320 "   -0.070 2.00e-02 2.50e+03   8.79e-02 9.65e+01
        pdb=" CG  ASN A 320 "    0.027 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 320 "   -0.009 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 320 "    0.151 2.00e-02 2.50e+03
        pdb=" C1  NAG A 804 "   -0.100 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 327 "   -0.021 2.00e-02 2.50e+03   2.17e-02 5.91e+00
        pdb=" CG  ASN A 327 "    0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 327 "    0.005 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 327 "    0.033 2.00e-02 2.50e+03
        pdb=" C1  NAG A 805 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1084 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 2208
        2.88 -     3.38: 5586
        3.38 -     3.89: 10177
        3.89 -     4.39: 11961
        4.39 -     4.90: 19506
  Nonbonded interactions: 49438
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 563 "
            pdb=" NZ  LYS A 286 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" NZ  LYS B 509 "
            pdb=" OD2 ASP B 517 "
     model   vdw
     2.382 3.120
  nonbonded pdb=" OG  SER B 537 "
            pdb=" O   VAL B 557 "
     model   vdw
     2.408 3.040
  nonbonded pdb=" NZ  LYS A  93 "
            pdb=" OE1 GLN A 386 "
     model   vdw
     2.430 3.120
  nonbonded pdb=" NZ  LYS B 427 "
            pdb=" O   SER B 474 "
     model   vdw
     2.499 3.120
  ... (remaining 49433 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:             1.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.450
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
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      :  0.012   0.089   6266  Z= 0.654
  Angle     :  1.286  24.209   8557  Z= 0.846
  Chirality :  0.085   0.854    951
  Planarity :  0.006   0.098   1078
  Dihedral  : 12.614 106.469   2342
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.23 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  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: -0.10 (0.27), residues: 763
  helix: -0.06 (0.23), residues: 395
  sheet:  0.67 (0.56), residues: 69
  loop : -0.01 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.004   TRP A 476 
 HIS   0.005   0.001   HIS A 239 
 PHE   0.015   0.003   PHE A 325 
 TYR   0.026   0.004   TYR B 504 
 ARG   0.004   0.001   ARG A 159 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05306 (    9)
  link_NAG-ASN         : angle       6.84032 (   27)
  link_BETA1-4         : bond        0.05398 (    3)
  link_BETA1-4         : angle       3.07642 (    9)
  hydrogen bonds       : bond        0.22306 (  332)
  hydrogen bonds       : angle       6.78582 (  930)
  SS BOND              : bond        0.04397 (    6)
  SS BOND              : angle       3.71837 (   12)
  covalent geometry    : bond        0.01127 ( 6248)
  covalent geometry    : angle       1.21814 ( 8509)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A   62 LYS cc_start: 0.7491 (mtpt) cc_final: 0.6778 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 1.2838
  time to fit residues: 138.4050
Evaluate side-chains
  66 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
A  99 GLN
A 395 ASN
A 440 GLN
A 491 HIS
A 532 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.172932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.135972 restraints weight = 5952.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 1.40
r_work: 0.3380 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   6266  Z= 0.183
  Angle     :  0.695  10.051   8557  Z= 0.357
  Chirality :  0.048   0.327    951
  Planarity :  0.005   0.034   1078
  Dihedral  :  6.932  59.215   1086
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.31 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  9.98 %
    Favored  : 88.17 %
  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:  1.05 (0.28), residues: 763
  helix:  1.20 (0.25), residues: 387
  sheet:  0.49 (0.52), residues: 74
  loop :  0.26 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 476 
 HIS   0.007   0.002   HIS A 239 
 PHE   0.014   0.002   PHE A 306 
 TYR   0.026   0.002   TYR A 383 
 ARG   0.004   0.001   ARG A 202 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00367 (    9)
  link_NAG-ASN         : angle       2.28056 (   27)
  link_BETA1-4         : bond        0.00534 (    3)
  link_BETA1-4         : angle       2.35774 (    9)
  hydrogen bonds       : bond        0.06326 (  332)
  hydrogen bonds       : angle       4.95886 (  930)
  SS BOND              : bond        0.00279 (    6)
  SS BOND              : angle       3.20292 (   12)
  covalent geometry    : bond        0.00407 ( 6248)
  covalent geometry    : angle       0.67049 ( 8509)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.726 
Fit side-chains
REVERT: B  508 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6865 (p0)
REVERT: A  121 MET cc_start: 0.8717 (mtm) cc_final: 0.8461 (mtp)
REVERT: A  180 LYS cc_start: 0.7590 (mttt) cc_final: 0.7164 (mtmp)
  outliers start: 10
  outliers final: 4
  residues processed: 87
  average time/residue: 1.2122
  time to fit residues: 110.7669
Evaluate side-chains
  73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  508 ASP
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue  554 LYS
Chi-restraints excluded: chain A residue  560 LYS
Chi-restraints excluded: chain A residue  577 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 71 optimal weight:    0.2980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 579 GLN
A  99 GLN
A 328 ASN
A 532 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.172208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.135001 restraints weight = 6012.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.40
r_work: 0.3430 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   6266  Z= 0.148
  Angle     :  0.619   8.832   8557  Z= 0.313
  Chirality :  0.048   0.304    951
  Planarity :  0.004   0.034   1078
  Dihedral  :  5.466  42.003   1086
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.70 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.83 %
    Favored  : 86.51 %
  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:  1.34 (0.29), residues: 763
  helix:  1.53 (0.26), residues: 390
  sheet:  0.54 (0.54), residues: 74
  loop :  0.26 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 476 
 HIS   0.008   0.001   HIS A 239 
 PHE   0.014   0.002   PHE A 521 
 TYR   0.019   0.001   TYR A 383 
 ARG   0.007   0.000   ARG A 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01209 (    9)
  link_NAG-ASN         : angle       2.31548 (   27)
  link_BETA1-4         : bond        0.00731 (    3)
  link_BETA1-4         : angle       1.91106 (    9)
  hydrogen bonds       : bond        0.05939 (  332)
  hydrogen bonds       : angle       4.62277 (  930)
  SS BOND              : bond        0.00519 (    6)
  SS BOND              : angle       3.01212 (   12)
  covalent geometry    : bond        0.00317 ( 6248)
  covalent geometry    : angle       0.59352 ( 8509)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7465 (mp)
  outliers start: 9
  outliers final: 2
  residues processed: 74
  average time/residue: 1.2139
  time to fit residues: 94.4628
Evaluate side-chains
  67 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  554 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 74 optimal weight:    0.3980
   chunk 66 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0270
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
B 579 GLN
A 524 GLN
A 532 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.170647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.137549 restraints weight = 6083.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.32
r_work: 0.3407 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   6266  Z= 0.146
  Angle     :  0.593   8.110   8557  Z= 0.302
  Chirality :  0.045   0.280    951
  Planarity :  0.004   0.035   1078
  Dihedral  :  4.648  39.766   1086
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.31 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.94 %
    Favored  : 85.21 %
  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:  1.37 (0.29), residues: 763
  helix:  1.54 (0.26), residues: 390
  sheet:  0.51 (0.56), residues: 74
  loop :  0.31 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 476 
 HIS   0.006   0.001   HIS A 239 
 PHE   0.015   0.002   PHE A 521 
 TYR   0.021   0.001   TYR A 383 
 ARG   0.002   0.000   ARG A 202 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00457 (    9)
  link_NAG-ASN         : angle       1.92756 (   27)
  link_BETA1-4         : bond        0.00498 (    3)
  link_BETA1-4         : angle       1.78121 (    9)
  hydrogen bonds       : bond        0.05695 (  332)
  hydrogen bonds       : angle       4.55768 (  930)
  SS BOND              : bond        0.00591 (    6)
  SS BOND              : angle       2.66235 (   12)
  covalent geometry    : bond        0.00328 ( 6248)
  covalent geometry    : angle       0.57350 ( 8509)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6676 (mm-30)
REVERT: A  150 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.5807 (mpt)
REVERT: A  330 MET cc_start: 0.7841 (ttt) cc_final: 0.7540 (ttm)
REVERT: A  429 ASP cc_start: 0.7421 (t0) cc_final: 0.7191 (t0)
REVERT: A  569 GLU cc_start: 0.8265 (tt0) cc_final: 0.8032 (tt0)
  outliers start: 10
  outliers final: 3
  residues processed: 80
  average time/residue: 1.2211
  time to fit residues: 102.8755
Evaluate side-chains
  73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  399 HIS
Chi-restraints excluded: chain A residue  560 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0470
   chunk 6 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0980
   chunk 12 optimal weight:    0.9980
   chunk 49 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 70 optimal weight:    0.1980
   chunk 29 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.3078

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

Flipped N/Q/H residues before XYZ refinement:
B 579 GLN
A 532 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.173651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.137109 restraints weight = 6065.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.39
r_work: 0.3398 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.3586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.065   6266  Z= 0.114
  Angle     :  0.527   8.763   8557  Z= 0.268
  Chirality :  0.042   0.269    951
  Planarity :  0.004   0.031   1078
  Dihedral  :  4.233  31.108   1086
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.31 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.31 %
    Favored  : 85.03 %
  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:  1.69 (0.30), residues: 763
  helix:  1.79 (0.26), residues: 391
  sheet:  0.61 (0.55), residues: 75
  loop :  0.48 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 163 
 HIS   0.005   0.001   HIS A 239 
 PHE   0.010   0.001   PHE A 521 
 TYR   0.014   0.001   TYR A 383 
 ARG   0.001   0.000   ARG A 587 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00405 (    9)
  link_NAG-ASN         : angle       1.77303 (   27)
  link_BETA1-4         : bond        0.00570 (    3)
  link_BETA1-4         : angle       1.50122 (    9)
  hydrogen bonds       : bond        0.04730 (  332)
  hydrogen bonds       : angle       4.36431 (  930)
  SS BOND              : bond        0.00621 (    6)
  SS BOND              : angle       2.77757 (   12)
  covalent geometry    : bond        0.00244 ( 6248)
  covalent geometry    : angle       0.50641 ( 8509)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  508 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6384 (p0)
REVERT: A   38 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6345 (mm-30)
REVERT: A  196 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7488 (p0)
REVERT: A  232 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7493 (mttt)
REVERT: A  330 MET cc_start: 0.7796 (ttt) cc_final: 0.7474 (ttm)
REVERT: A  429 ASP cc_start: 0.7397 (t0) cc_final: 0.7142 (t0)
REVERT: A  569 GLU cc_start: 0.8236 (tt0) cc_final: 0.7974 (tt0)
  outliers start: 9
  outliers final: 3
  residues processed: 78
  average time/residue: 1.0959
  time to fit residues: 90.3757
Evaluate side-chains
  73 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  508 ASP
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  399 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0170
   chunk 47 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 48 optimal weight:    0.3980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
B 579 GLN
A 532 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.182212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.151886 restraints weight = 5699.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.15
r_work: 0.3431 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.3701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   6266  Z= 0.131
  Angle     :  0.563   9.270   8557  Z= 0.287
  Chirality :  0.044   0.316    951
  Planarity :  0.004   0.033   1078
  Dihedral  :  4.158  21.880   1086
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.31 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.31 %
    Favored  : 84.66 %
  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:  1.73 (0.30), residues: 763
  helix:  1.78 (0.26), residues: 391
  sheet:  0.75 (0.56), residues: 75
  loop :  0.55 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 476 
 HIS   0.006   0.001   HIS A 239 
 PHE   0.016   0.001   PHE A 521 
 TYR   0.020   0.001   TYR A 383 
 ARG   0.002   0.000   ARG A 202 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00368 (    9)
  link_NAG-ASN         : angle       1.77647 (   27)
  link_BETA1-4         : bond        0.00537 (    3)
  link_BETA1-4         : angle       1.55738 (    9)
  hydrogen bonds       : bond        0.05236 (  332)
  hydrogen bonds       : angle       4.37226 (  930)
  SS BOND              : bond        0.00570 (    6)
  SS BOND              : angle       2.94928 (   12)
  covalent geometry    : bond        0.00294 ( 6248)
  covalent geometry    : angle       0.54194 ( 8509)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  449 ARG cc_start: 0.6704 (mtp85) cc_final: 0.6403 (mtp85)
REVERT: A   38 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6514 (mm-30)
REVERT: A  150 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.5767 (mpt)
REVERT: A  232 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7546 (mttt)
REVERT: A  330 MET cc_start: 0.7924 (ttt) cc_final: 0.7628 (ttm)
REVERT: A  429 ASP cc_start: 0.7407 (t0) cc_final: 0.7205 (t0)
REVERT: A  569 GLU cc_start: 0.8142 (tt0) cc_final: 0.7901 (tt0)
  outliers start: 11
  outliers final: 3
  residues processed: 80
  average time/residue: 1.2115
  time to fit residues: 102.3260
Evaluate side-chains
  74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  399 HIS
Chi-restraints excluded: chain A residue  560 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0030
   chunk 9 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 69 optimal weight:    4.9990
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
B 579 GLN
A 193 ASN
A 532 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.171503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.134601 restraints weight = 6000.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.41
r_work: 0.3368 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.3845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   6266  Z= 0.128
  Angle     :  0.560  11.101   8557  Z= 0.285
  Chirality :  0.043   0.314    951
  Planarity :  0.004   0.032   1078
  Dihedral  :  4.097  22.489   1086
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.44 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.42 %
    Favored  : 84.29 %
  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:  1.79 (0.30), residues: 763
  helix:  1.79 (0.26), residues: 391
  sheet:  0.83 (0.56), residues: 75
  loop :  0.61 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 476 
 HIS   0.006   0.001   HIS A 239 
 PHE   0.014   0.001   PHE A 521 
 TYR   0.018   0.001   TYR A 383 
 ARG   0.007   0.000   ARG A 587 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00377 (    9)
  link_NAG-ASN         : angle       1.74946 (   27)
  link_BETA1-4         : bond        0.00523 (    3)
  link_BETA1-4         : angle       1.54518 (    9)
  hydrogen bonds       : bond        0.05072 (  332)
  hydrogen bonds       : angle       4.37569 (  930)
  SS BOND              : bond        0.00583 (    6)
  SS BOND              : angle       3.07831 (   12)
  covalent geometry    : bond        0.00287 ( 6248)
  covalent geometry    : angle       0.53812 ( 8509)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  449 ARG cc_start: 0.6643 (mtp85) cc_final: 0.6349 (mtp85)
REVERT: A   36 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7271 (tp30)
REVERT: A   38 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6485 (mm-30)
REVERT: A  150 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.5739 (mpt)
REVERT: A  330 MET cc_start: 0.7922 (ttt) cc_final: 0.7577 (ttm)
REVERT: A  569 GLU cc_start: 0.8171 (tt0) cc_final: 0.7907 (tt0)
  outliers start: 7
  outliers final: 2
  residues processed: 79
  average time/residue: 1.2212
  time to fit residues: 101.7381
Evaluate side-chains
  75 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  399 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.1980
   chunk 23 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0670
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN
B 579 GLN
A 532 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.172206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.135497 restraints weight = 6005.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 1.40
r_work: 0.3382 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   6266  Z= 0.120
  Angle     :  0.554  12.958   8557  Z= 0.281
  Chirality :  0.043   0.322    951
  Planarity :  0.004   0.033   1078
  Dihedral  :  3.999  24.682   1086
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.44 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 15.16 %
    Favored  : 83.36 %
  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:  1.89 (0.30), residues: 763
  helix:  1.86 (0.26), residues: 391
  sheet:  0.84 (0.57), residues: 75
  loop :  0.69 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 239 
 PHE   0.013   0.001   PHE A 521 
 TYR   0.017   0.001   TYR A 383 
 ARG   0.006   0.000   ARG A 587 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00367 (    9)
  link_NAG-ASN         : angle       1.71032 (   27)
  link_BETA1-4         : bond        0.00470 (    3)
  link_BETA1-4         : angle       1.48771 (    9)
  hydrogen bonds       : bond        0.04870 (  332)
  hydrogen bonds       : angle       4.31515 (  930)
  SS BOND              : bond        0.00707 (    6)
  SS BOND              : angle       2.93256 (   12)
  covalent geometry    : bond        0.00266 ( 6248)
  covalent geometry    : angle       0.53378 ( 8509)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  449 ARG cc_start: 0.6660 (mtp85) cc_final: 0.6375 (mtp85)
REVERT: A   36 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7280 (tp30)
REVERT: A   38 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6477 (mm-30)
REVERT: A  150 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.5730 (mpt)
REVERT: A  196 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7567 (p0)
REVERT: A  232 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7594 (mttt)
REVERT: A  330 MET cc_start: 0.7898 (ttt) cc_final: 0.7583 (ttm)
REVERT: A  569 GLU cc_start: 0.8113 (tt0) cc_final: 0.7903 (tt0)
  outliers start: 8
  outliers final: 3
  residues processed: 77
  average time/residue: 1.1167
  time to fit residues: 90.6963
Evaluate side-chains
  70 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  399 HIS
Chi-restraints excluded: chain A residue  560 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3974 r_free = 0.3974 target = 0.180334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.149944 restraints weight = 5752.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.18
r_work: 0.3402 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081   6266  Z= 0.153
  Angle     :  0.612  15.374   8557  Z= 0.311
  Chirality :  0.045   0.344    951
  Planarity :  0.004   0.034   1078
  Dihedral  :  4.208  29.066   1086
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.44 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 15.90 %
    Favored  : 82.81 %
  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:  1.70 (0.30), residues: 763
  helix:  1.68 (0.26), residues: 388
  sheet:  0.87 (0.55), residues: 80
  loop :  0.62 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 476 
 HIS   0.007   0.001   HIS A 239 
 PHE   0.017   0.002   PHE A 521 
 TYR   0.020   0.001   TYR A 383 
 ARG   0.005   0.000   ARG A 587 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00354 (    9)
  link_NAG-ASN         : angle       1.81337 (   27)
  link_BETA1-4         : bond        0.00529 (    3)
  link_BETA1-4         : angle       1.60022 (    9)
  hydrogen bonds       : bond        0.05674 (  332)
  hydrogen bonds       : angle       4.45270 (  930)
  SS BOND              : bond        0.00734 (    6)
  SS BOND              : angle       3.10894 (   12)
  covalent geometry    : bond        0.00355 ( 6248)
  covalent geometry    : angle       0.59158 ( 8509)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  449 ARG cc_start: 0.6634 (mtp85) cc_final: 0.6382 (mtp85)
REVERT: A   38 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6636 (mm-30)
REVERT: A  150 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.5820 (mpt)
REVERT: A  232 LYS cc_start: 0.8297 (mtpt) cc_final: 0.8003 (mttt)
REVERT: A  569 GLU cc_start: 0.8167 (tt0) cc_final: 0.7922 (tt0)
  outliers start: 7
  outliers final: 4
  residues processed: 76
  average time/residue: 1.2088
  time to fit residues: 96.7456
Evaluate side-chains
  77 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  181 TYR
Chi-restraints excluded: chain A residue  399 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.180152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.149059 restraints weight = 5809.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.44
r_work: 0.3375 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.4102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078   6266  Z= 0.149
  Angle     :  0.608  15.212   8557  Z= 0.309
  Chirality :  0.045   0.336    951
  Planarity :  0.004   0.034   1078
  Dihedral  :  4.263  28.970   1086
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.44 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 16.45 %
    Favored  : 82.62 %
  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:  1.67 (0.30), residues: 763
  helix:  1.72 (0.26), residues: 382
  sheet:  0.96 (0.56), residues: 78
  loop :  0.51 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 476 
 HIS   0.008   0.001   HIS A 239 
 PHE   0.015   0.002   PHE A 521 
 TYR   0.019   0.001   TYR A 383 
 ARG   0.005   0.000   ARG A 587 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00356 (    9)
  link_NAG-ASN         : angle       1.83161 (   27)
  link_BETA1-4         : bond        0.00475 (    3)
  link_BETA1-4         : angle       1.60075 (    9)
  hydrogen bonds       : bond        0.05590 (  332)
  hydrogen bonds       : angle       4.45838 (  930)
  SS BOND              : bond        0.00690 (    6)
  SS BOND              : angle       3.01122 (   12)
  covalent geometry    : bond        0.00344 ( 6248)
  covalent geometry    : angle       0.58799 ( 8509)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  449 ARG cc_start: 0.6750 (mtp85) cc_final: 0.6519 (mtp85)
REVERT: A   36 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7355 (tp30)
REVERT: A   38 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6714 (mm-30)
REVERT: A  150 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.5854 (mpt)
REVERT: A  232 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8086 (mttt)
REVERT: A  569 GLU cc_start: 0.8214 (tt0) cc_final: 0.7996 (tt0)
  outliers start: 5
  outliers final: 2
  residues processed: 74
  average time/residue: 1.1442
  time to fit residues: 89.2131
Evaluate side-chains
  74 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain A residue  150 MET
Chi-restraints excluded: chain A residue  399 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.168562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.135976 restraints weight = 6170.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.49
r_work: 0.3370 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   6266  Z= 0.164
  Angle     :  0.631  15.013   8557  Z= 0.321
  Chirality :  0.046   0.346    951
  Planarity :  0.005   0.035   1078
  Dihedral  :  4.410  29.874   1086
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.44 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 16.45 %
    Favored  : 82.81 %
  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:  1.54 (0.30), residues: 763
  helix:  1.62 (0.26), residues: 382
  sheet:  0.89 (0.55), residues: 78
  loop :  0.44 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 476 
 HIS   0.008   0.001   HIS A 239 
 PHE   0.017   0.002   PHE A 521 
 TYR   0.021   0.002   TYR A 383 
 ARG   0.004   0.000   ARG A 587 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00350 (    9)
  link_NAG-ASN         : angle       1.88641 (   27)
  link_BETA1-4         : bond        0.00477 (    3)
  link_BETA1-4         : angle       1.63230 (    9)
  hydrogen bonds       : bond        0.05961 (  332)
  hydrogen bonds       : angle       4.52083 (  930)
  SS BOND              : bond        0.00718 (    6)
  SS BOND              : angle       2.98781 (   12)
  covalent geometry    : bond        0.00381 ( 6248)
  covalent geometry    : angle       0.61161 ( 8509)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5104.71 seconds
wall clock time: 88 minutes 30.85 seconds (5310.85 seconds total)