Starting phenix.real_space_refine
on Thu Jul 24 22:17:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dlv_27517/07_2025/8dlv_27517.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dlv_27517/07_2025/8dlv_27517.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dlv_27517/07_2025/8dlv_27517.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dlv_27517/07_2025/8dlv_27517.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dlv_27517/07_2025/8dlv_27517.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dlv_27517/07_2025/8dlv_27517.cif"
  }
  resolution = 3.11
  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=  -0.001 sd=   0.028
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      37      5.16       5
     C    4186      2.51       5
     N    1081      2.21       5
     O    1249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6553
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1593
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      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: 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: "E"
      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: 4.78, per 1000 atoms: 0.73
  Number of scatterers: 6553
  At special positions: 0
  Unit cell: (81, 83, 122, 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    1249      8.00
     N    1081      7.00
     C    4186      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 530 " - pdb=" SG  CYS E 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
    NAG-ASN
      " NAG B1301 " - " ASN B 343 "
      " NAG E 701 " - " ASN E  53 "
      " NAG E 702 " - " ASN E  90 "
      " NAG E 703 " - " ASN E 103 "
      " NAG E 704 " - " ASN E 322 "
      " NAG E 705 " - " ASN E 432 "
      " NAG E 706 " - " ASN E 546 "
  Time building additional restraints: 1.37
  Conformation dependent library (CDL) restraints added in 826.3 milliseconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 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:
      40 helices and 6 sheets defined
      58.5% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 4.358A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.448A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.667A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 505
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 4.004A  pdb=" N   ASN E  33 " --> pdb=" O   LEU E  29 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   HIS E  34 " --> pdb=" O   ASP E  30 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
      removed outlier: 3.611A  pdb=" N   GLN E  81 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 82 through 83
      No H-bonds generated for 'chain 'E' and resid 82 through 83'
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.721A  pdb=" N   GLU E  87 " --> pdb=" O   PRO E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 101
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 4.033A  pdb=" N   VAL E 107 " --> pdb=" O   GLY E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 129
    Processing helix  chain 'E' and resid 143 through 155
      removed outlier: 3.881A  pdb=" N   MET E 152 " --> pdb=" O   LEU E 148 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   ALA E 153 " --> pdb=" O   ASN E 149 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASN E 154 " --> pdb=" O   GLU E 150 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.718A  pdb=" N   VAL E 185 " --> pdb=" O   GLU E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 205
    Processing helix  chain 'E' and resid 206 through 208
      No H-bonds generated for 'chain 'E' and resid 206 through 208'
    Processing helix  chain 'E' and resid 218 through 252
      removed outlier: 3.764A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLU E 232 " --> pdb=" O   HIS E 228 " (cutoff:3.500A)
      Proline residue:  E 235  - end of helix
    Processing helix  chain 'E' and resid 265 through 267
      No H-bonds generated for 'chain 'E' and resid 265 through 267'
    Processing helix  chain 'E' and resid 275 through 279
      removed outlier: 3.784A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 300
    Processing helix  chain 'E' and resid 303 through 319
    Processing helix  chain 'E' and resid 324 through 331
      removed outlier: 3.632A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.671A  pdb=" N   TYR E 385 " --> pdb=" O   TYR E 381 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 388
      No H-bonds generated for 'chain 'E' and resid 386 through 388'
    Processing helix  chain 'E' and resid 389 through 393
    Processing helix  chain 'E' and resid 397 through 413
      removed outlier: 4.197A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   MET E 408 " --> pdb=" O   VAL E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 421
    Processing helix  chain 'E' and resid 431 through 447
      removed outlier: 3.527A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.320A  pdb=" N   PHE E 452 " --> pdb=" O   GLY E 448 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 469 through 471
      No H-bonds generated for 'chain 'E' and resid 469 through 471'
    Processing helix  chain 'E' and resid 472 through 484
    Processing helix  chain 'E' and resid 499 through 502
      removed outlier: 3.595A  pdb=" N   SER E 502 " --> pdb=" O   ASP E 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 499 through 502'
    Processing helix  chain 'E' and resid 503 through 508
    Processing helix  chain 'E' and resid 512 through 533
      removed outlier: 4.474A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.902A  pdb=" N   MET E 557 " --> pdb=" O   LYS E 553 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 565 through 574
    Processing helix  chain 'E' and resid 581 through 588
    Processing helix  chain 'E' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.995A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'E' and resid 262 through 263
      removed outlier: 6.092A  pdb=" N   LEU E 262 " --> pdb=" O   VAL E 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 347 through 352
      removed outlier: 6.075A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    912 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: 1.63

  Time building geometry restraints manager: 1.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2088
        1.35 -     1.47: 1815
        1.47 -     1.60: 2774
        1.60 -     1.73: 0
        1.73 -     1.85: 58
  Bond restraints: 6735
  Sorted by residual:
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.465 -0.059 2.00e-02 2.50e+03 8.67e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.459 -0.053 2.00e-02 2.50e+03 7.03e+00
  bond pdb=" C1  NAG E 706 "
       pdb=" O5  NAG E 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.455 -0.049 2.00e-02 2.50e+03 6.03e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.455 -0.049 2.00e-02 2.50e+03 5.98e+00
  bond pdb=" C   GLU E 145 "
       pdb=" N   PRO E 146 "
    ideal  model  delta    sigma   weight residual
    1.335  1.367 -0.032 1.38e-02 5.25e+03 5.31e+00
  ... (remaining 6730 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 8761
        2.01 -     4.02: 349
        4.02 -     6.03: 30
        6.03 -     8.04: 11
        8.04 -    10.04: 1
  Bond angle restraints: 9152
  Sorted by residual:
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.36  128.16   -5.80 1.42e+00 4.96e-01 1.67e+01
  angle pdb=" CA  ASN E 437 "
        pdb=" CB  ASN E 437 "
        pdb=" CG  ASN E 437 "
      ideal   model   delta    sigma   weight residual
     112.60  116.24   -3.64 1.00e+00 1.00e+00 1.32e+01
  angle pdb=" CA  TYR B 495 "
        pdb=" CB  TYR B 495 "
        pdb=" CG  TYR B 495 "
      ideal   model   delta    sigma   weight residual
     113.90  120.12   -6.22 1.80e+00 3.09e-01 1.20e+01
  angle pdb=" CA  CYS E 133 "
        pdb=" CB  CYS E 133 "
        pdb=" SG  CYS E 133 "
      ideal   model   delta    sigma   weight residual
     114.40  122.20   -7.80 2.30e+00 1.89e-01 1.15e+01
  angle pdb=" CA  ASN B 360 "
        pdb=" CB  ASN B 360 "
        pdb=" CG  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     112.60  115.95   -3.35 1.00e+00 1.00e+00 1.12e+01
  ... (remaining 9147 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 3687
       17.07 -    34.14: 301
       34.14 -    51.21: 56
       51.21 -    68.27: 14
       68.27 -    85.34: 10
  Dihedral angle restraints: 4068
    sinusoidal: 1730
      harmonic: 2338
  Sorted by residual:
  dihedral pdb=" CB  CYS E 133 "
           pdb=" SG  CYS E 133 "
           pdb=" SG  CYS E 141 "
           pdb=" CB  CYS E 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -51.15  -34.85     1      1.00e+01 1.00e-02 1.72e+01
  dihedral pdb=" SG  CYS B 391 "
           pdb=" CB  CYS B 525 "
           pdb=" SG  CYS B 525 "
           pdb=" CA  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   15.84   63.16     1      2.00e+01 2.50e-03 1.32e+01
  dihedral pdb=" C   ASN B 360 "
           pdb=" N   ASN B 360 "
           pdb=" CA  ASN B 360 "
           pdb=" CB  ASN B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.24    8.64     0      2.50e+00 1.60e-01 1.19e+01
  ... (remaining 4065 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 711
       0.055 -    0.110: 198
       0.110 -    0.165: 56
       0.165 -    0.220: 10
       0.220 -    0.275: 2
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.28 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CB  VAL E 581 "
            pdb=" CA  VAL E 581 "
            pdb=" CG1 VAL E 581 "
            pdb=" CG2 VAL E 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.87e+00
  chirality pdb=" CA  ASN E 437 "
            pdb=" N   ASN E 437 "
            pdb=" C   ASN E 437 "
            pdb=" CB  ASN E 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 974 not shown)

  Planarity restraints: 1185
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.050 5.00e-02 4.00e+02   7.53e-02 9.07e+00
        pdb=" N   PRO E 590 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR E  41 "    0.015 2.00e-02 2.50e+03   2.94e-02 8.61e+00
        pdb=" C   TYR E  41 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   TYR E  41 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLN E  42 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 499 "   -0.047 5.00e-02 4.00e+02   7.07e-02 8.00e+00
        pdb=" N   PRO E 500 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO E 500 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO E 500 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 1182 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2049
        2.83 -     3.35: 5939
        3.35 -     3.86: 11341
        3.86 -     4.38: 12913
        4.38 -     4.90: 22190
  Nonbonded interactions: 54432
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   ASP E 367 "
            pdb=" OG1 THR E 371 "
     model   vdw
     2.367 3.040
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" OH  TYR E 237 "
            pdb=" O   VAL E 485 "
     model   vdw
     2.374 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.406 3.040
  ... (remaining 54427 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:             3.460
  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:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.120
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
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      :  0.006   0.070   6748  Z= 0.259
  Angle     :  0.914  12.322   9185  Z= 0.508
  Chirality :  0.058   0.275    977
  Planarity :  0.008   0.075   1178
  Dihedral  : 13.400  85.343   2550
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  4.29 %
    Favored  : 95.43 %
  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: -0.25 (0.25), residues: 793
  helix:  0.20 (0.22), residues: 393
  sheet:  1.13 (0.73), residues: 43
  loop : -0.64 (0.28), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E  69 
 HIS   0.005   0.001   HIS E 378 
 PHE   0.028   0.003   PHE E 369 
 TYR   0.033   0.002   TYR B 495 
 ARG   0.014   0.001   ARG E 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00762 (    7)
  link_NAG-ASN         : angle       4.64038 (   21)
  hydrogen bonds       : bond        0.14584 (  321)
  hydrogen bonds       : angle       6.23743 (  912)
  SS BOND              : bond        0.00660 (    6)
  SS BOND              : angle       2.32356 (   12)
  covalent geometry    : bond        0.00564 ( 6735)
  covalent geometry    : angle       0.88417 ( 9152)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
REVERT: B  420 ASP cc_start: 0.8498 (m-30) cc_final: 0.8282 (m-30)
REVERT: E  367 ASP cc_start: 0.8696 (m-30) cc_final: 0.8448 (p0)
  outliers start: 2
  outliers final: 1
  residues processed: 121
  average time/residue: 0.2493
  time to fit residues: 37.7926
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   34 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.0050
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 40 optimal weight:    0.2980
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
B 394 ASN
B 437 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 345 HIS
** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 552 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.069771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.055981 restraints weight = 18644.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 3.20
r_work: 0.2778 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6748  Z= 0.129
  Angle     :  0.574   7.308   9185  Z= 0.288
  Chirality :  0.040   0.143    977
  Planarity :  0.005   0.042   1178
  Dihedral  :  5.370  52.518   1015
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  7.86 %
    Favored  : 91.29 %
  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:  0.80 (0.28), residues: 793
  helix:  1.25 (0.25), residues: 404
  sheet:  1.09 (0.72), residues: 42
  loop : -0.32 (0.31), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 345 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.017   0.001   TYR B 495 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00490 (    7)
  link_NAG-ASN         : angle       3.00549 (   21)
  hydrogen bonds       : bond        0.04444 (  321)
  hydrogen bonds       : angle       4.67075 (  912)
  SS BOND              : bond        0.00302 (    6)
  SS BOND              : angle       1.59101 (   12)
  covalent geometry    : bond        0.00280 ( 6735)
  covalent geometry    : angle       0.55420 ( 9152)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
REVERT: E  182 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8753 (mm-30)
REVERT: E  367 ASP cc_start: 0.9111 (m-30) cc_final: 0.8724 (p0)
  outliers start: 6
  outliers final: 4
  residues processed: 71
  average time/residue: 0.1996
  time to fit residues: 19.0358
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0030
   chunk 39 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.068654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.054549 restraints weight = 18779.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 3.26
r_work: 0.2740 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6748  Z= 0.137
  Angle     :  0.533   6.514   9185  Z= 0.269
  Chirality :  0.040   0.139    977
  Planarity :  0.004   0.043   1178
  Dihedral  :  4.746  53.917   1013
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.57 %
    Favored  : 90.29 %
  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:  1.32 (0.29), residues: 793
  helix:  1.65 (0.26), residues: 402
  sheet:  0.94 (0.75), residues: 43
  loop :  0.02 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 239 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.013   0.001   TYR B 495 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00385 (    7)
  link_NAG-ASN         : angle       2.51741 (   21)
  hydrogen bonds       : bond        0.04242 (  321)
  hydrogen bonds       : angle       4.44041 (  912)
  SS BOND              : bond        0.00287 (    6)
  SS BOND              : angle       1.25781 (   12)
  covalent geometry    : bond        0.00300 ( 6735)
  covalent geometry    : angle       0.51791 ( 9152)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
REVERT: E  182 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8770 (mm-30)
REVERT: E  270 MET cc_start: 0.9388 (tpt) cc_final: 0.8579 (tpp)
REVERT: E  291 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8155 (mm)
REVERT: E  325 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8293 (mm-40)
REVERT: E  367 ASP cc_start: 0.9128 (m-30) cc_final: 0.8715 (p0)
  outliers start: 8
  outliers final: 6
  residues processed: 65
  average time/residue: 0.2127
  time to fit residues: 18.4902
Evaluate side-chains
  63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 68 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** 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 = 0.3213 r_free = 0.3213 target = 0.068238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.054227 restraints weight = 19000.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 3.24
r_work: 0.2731 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6748  Z= 0.136
  Angle     :  0.508   5.450   9185  Z= 0.258
  Chirality :  0.040   0.157    977
  Planarity :  0.004   0.038   1178
  Dihedral  :  4.578  54.693   1013
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.71 %
    Favored  : 89.00 %
  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:  1.47 (0.29), residues: 793
  helix:  1.78 (0.26), residues: 399
  sheet:  1.12 (0.78), residues: 42
  loop :  0.09 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.019   0.001   TYR E 613 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00339 (    7)
  link_NAG-ASN         : angle       2.19933 (   21)
  hydrogen bonds       : bond        0.04111 (  321)
  hydrogen bonds       : angle       4.36071 (  912)
  SS BOND              : bond        0.00269 (    6)
  SS BOND              : angle       1.16875 (   12)
  covalent geometry    : bond        0.00300 ( 6735)
  covalent geometry    : angle       0.49562 ( 9152)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
REVERT: B  403 ARG cc_start: 0.8939 (mtm110) cc_final: 0.8724 (mtm110)
REVERT: B  458 LYS cc_start: 0.9373 (mppt) cc_final: 0.9100 (mmtm)
REVERT: E  152 MET cc_start: 0.8696 (mmt) cc_final: 0.8453 (mmt)
REVERT: E  182 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8753 (mm-30)
REVERT: E  270 MET cc_start: 0.9340 (tpt) cc_final: 0.8392 (tpp)
REVERT: E  291 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8092 (mm)
REVERT: E  367 ASP cc_start: 0.9157 (m-30) cc_final: 0.8752 (p0)
  outliers start: 9
  outliers final: 6
  residues processed: 66
  average time/residue: 0.2309
  time to fit residues: 20.1629
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** 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 = 0.3193 r_free = 0.3193 target = 0.067365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.053365 restraints weight = 18814.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 3.20
r_work: 0.2718 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6748  Z= 0.145
  Angle     :  0.508   5.345   9185  Z= 0.260
  Chirality :  0.040   0.152    977
  Planarity :  0.004   0.038   1178
  Dihedral  :  4.505  55.025   1013
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 11.29 %
    Favored  : 87.00 %
  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:  1.59 (0.29), residues: 793
  helix:  1.88 (0.26), residues: 398
  sheet:  1.15 (0.78), residues: 42
  loop :  0.16 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.010   0.001   TYR B 495 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00316 (    7)
  link_NAG-ASN         : angle       2.04014 (   21)
  hydrogen bonds       : bond        0.04113 (  321)
  hydrogen bonds       : angle       4.36910 (  912)
  SS BOND              : bond        0.00290 (    6)
  SS BOND              : angle       1.13648 (   12)
  covalent geometry    : bond        0.00324 ( 6735)
  covalent geometry    : angle       0.49765 ( 9152)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.694 
Fit side-chains
REVERT: B  458 LYS cc_start: 0.9406 (mppt) cc_final: 0.9125 (mmtm)
REVERT: E  182 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8753 (mm-30)
REVERT: E  270 MET cc_start: 0.9314 (tpt) cc_final: 0.8395 (tpp)
REVERT: E  291 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8201 (mm)
REVERT: E  367 ASP cc_start: 0.9177 (m-30) cc_final: 0.8780 (p0)
  outliers start: 12
  outliers final: 9
  residues processed: 66
  average time/residue: 0.2218
  time to fit residues: 19.2022
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  261 CYS
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  604 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** 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 = 0.3199 r_free = 0.3199 target = 0.067665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.053799 restraints weight = 18583.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 3.17
r_work: 0.2719 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6748  Z= 0.136
  Angle     :  0.501   6.522   9185  Z= 0.254
  Chirality :  0.040   0.156    977
  Planarity :  0.004   0.037   1178
  Dihedral  :  4.482  55.604   1013
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.71 %
    Favored  : 86.71 %
  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: 793
  helix:  1.94 (0.26), residues: 398
  sheet:  0.95 (0.77), residues: 42
  loop :  0.24 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.032   0.001   TYR E 613 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00285 (    7)
  link_NAG-ASN         : angle       1.97814 (   21)
  hydrogen bonds       : bond        0.04029 (  321)
  hydrogen bonds       : angle       4.32280 (  912)
  SS BOND              : bond        0.00209 (    6)
  SS BOND              : angle       0.71755 (   12)
  covalent geometry    : bond        0.00304 ( 6735)
  covalent geometry    : angle       0.49238 ( 9152)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.758 
Fit side-chains
REVERT: B  458 LYS cc_start: 0.9410 (mppt) cc_final: 0.9116 (mmtm)
REVERT: E   55 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7948 (p)
REVERT: E  182 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8746 (mm-30)
REVERT: E  270 MET cc_start: 0.9250 (tpt) cc_final: 0.8462 (tpp)
REVERT: E  291 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8218 (mm)
REVERT: E  367 ASP cc_start: 0.9144 (m-30) cc_final: 0.8753 (p0)
  outliers start: 11
  outliers final: 8
  residues processed: 64
  average time/residue: 0.1983
  time to fit residues: 17.4610
Evaluate side-chains
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  261 CYS
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  604 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** 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 = 0.3162 r_free = 0.3162 target = 0.065824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.051778 restraints weight = 18899.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 3.19
r_work: 0.2668 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6748  Z= 0.200
  Angle     :  0.545   5.511   9185  Z= 0.278
  Chirality :  0.041   0.153    977
  Planarity :  0.004   0.033   1178
  Dihedral  :  4.676  56.572   1013
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.00 %
    Favored  : 86.29 %
  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:  1.64 (0.30), residues: 793
  helix:  1.87 (0.26), residues: 400
  sheet:  0.88 (0.79), residues: 42
  loop :  0.30 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.018   0.001   PHE E 369 
 TYR   0.016   0.001   TYR B 495 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00286 (    7)
  link_NAG-ASN         : angle       2.03555 (   21)
  hydrogen bonds       : bond        0.04405 (  321)
  hydrogen bonds       : angle       4.43566 (  912)
  SS BOND              : bond        0.00262 (    6)
  SS BOND              : angle       0.84164 (   12)
  covalent geometry    : bond        0.00450 ( 6735)
  covalent geometry    : angle       0.53584 ( 9152)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.700 
Fit side-chains
REVERT: E  182 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8792 (mm-30)
REVERT: E  291 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8203 (mm)
REVERT: E  367 ASP cc_start: 0.9152 (m-30) cc_final: 0.8772 (p0)
REVERT: E  474 MET cc_start: 0.9010 (mmp) cc_final: 0.8659 (mmm)
REVERT: E  613 TYR cc_start: 0.6857 (t80) cc_final: 0.6462 (t80)
  outliers start: 12
  outliers final: 8
  residues processed: 61
  average time/residue: 0.1896
  time to fit residues: 15.9890
Evaluate side-chains
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  261 CYS
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  604 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0670
   chunk 62 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** 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 = 0.3186 r_free = 0.3186 target = 0.067022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.053008 restraints weight = 18814.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 3.17
r_work: 0.2712 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6748  Z= 0.123
  Angle     :  0.493   5.493   9185  Z= 0.251
  Chirality :  0.040   0.154    977
  Planarity :  0.003   0.036   1178
  Dihedral  :  4.506  56.113   1013
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.43 %
    Favored  : 86.29 %
  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:  1.67 (0.30), residues: 793
  helix:  1.90 (0.26), residues: 398
  sheet:  0.83 (0.80), residues: 42
  loop :  0.33 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.009   0.001   TYR B 495 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00289 (    7)
  link_NAG-ASN         : angle       1.97221 (   21)
  hydrogen bonds       : bond        0.04004 (  321)
  hydrogen bonds       : angle       4.36006 (  912)
  SS BOND              : bond        0.00211 (    6)
  SS BOND              : angle       0.92318 (   12)
  covalent geometry    : bond        0.00272 ( 6735)
  covalent geometry    : angle       0.48388 ( 9152)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.833 
Fit side-chains
REVERT: E  182 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8757 (mm-30)
REVERT: E  270 MET cc_start: 0.9317 (tpt) cc_final: 0.9114 (tpp)
REVERT: E  291 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8233 (mm)
REVERT: E  367 ASP cc_start: 0.9151 (m-30) cc_final: 0.8749 (p0)
  outliers start: 9
  outliers final: 7
  residues processed: 62
  average time/residue: 0.1914
  time to fit residues: 16.3578
Evaluate side-chains
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  261 CYS
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  604 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    0.3980
   chunk 41 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0370
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** 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 = 0.3192 r_free = 0.3192 target = 0.067267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.053232 restraints weight = 18957.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 3.20
r_work: 0.2715 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6748  Z= 0.126
  Angle     :  0.498   6.940   9185  Z= 0.253
  Chirality :  0.040   0.154    977
  Planarity :  0.003   0.038   1178
  Dihedral  :  4.467  56.216   1013
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.86 %
    Favored  : 86.00 %
  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:  1.68 (0.30), residues: 793
  helix:  1.89 (0.26), residues: 398
  sheet:  0.77 (0.80), residues: 42
  loop :  0.37 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.010   0.001   TYR B 495 
 ARG   0.003   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00281 (    7)
  link_NAG-ASN         : angle       1.93951 (   21)
  hydrogen bonds       : bond        0.03971 (  321)
  hydrogen bonds       : angle       4.35006 (  912)
  SS BOND              : bond        0.00214 (    6)
  SS BOND              : angle       0.89343 (   12)
  covalent geometry    : bond        0.00280 ( 6735)
  covalent geometry    : angle       0.48902 ( 9152)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.710 
Fit side-chains
REVERT: E  182 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8761 (mm-30)
REVERT: E  291 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8243 (mm)
REVERT: E  367 ASP cc_start: 0.9153 (m-30) cc_final: 0.8721 (p0)
  outliers start: 8
  outliers final: 6
  residues processed: 60
  average time/residue: 0.1940
  time to fit residues: 15.9200
Evaluate side-chains
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  261 CYS
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  604 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    0.2980
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 2 optimal weight:    0.4980
   chunk 50 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** 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 = 0.3200 r_free = 0.3200 target = 0.067567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.053681 restraints weight = 18983.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 3.19
r_work: 0.2716 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6748  Z= 0.132
  Angle     :  0.499   5.449   9185  Z= 0.254
  Chirality :  0.040   0.154    977
  Planarity :  0.003   0.038   1178
  Dihedral  :  4.460  56.220   1013
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.43 %
    Favored  : 86.43 %
  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:  1.74 (0.30), residues: 793
  helix:  1.92 (0.26), residues: 396
  sheet:  0.74 (0.80), residues: 42
  loop :  0.43 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.037   0.001   TYR E 613 
 ARG   0.003   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00278 (    7)
  link_NAG-ASN         : angle       1.94429 (   21)
  hydrogen bonds       : bond        0.03964 (  321)
  hydrogen bonds       : angle       4.35069 (  912)
  SS BOND              : bond        0.00217 (    6)
  SS BOND              : angle       0.89069 (   12)
  covalent geometry    : bond        0.00292 ( 6735)
  covalent geometry    : angle       0.49023 ( 9152)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.777 
Fit side-chains
REVERT: E  182 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8789 (mm-30)
REVERT: E  291 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8141 (mm)
REVERT: E  367 ASP cc_start: 0.9129 (m-30) cc_final: 0.8750 (p0)
  outliers start: 8
  outliers final: 7
  residues processed: 61
  average time/residue: 0.1956
  time to fit residues: 16.3560
Evaluate side-chains
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  261 CYS
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  604 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** 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 = 0.3192 r_free = 0.3192 target = 0.067131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.053156 restraints weight = 19167.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 3.21
r_work: 0.2703 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6748  Z= 0.147
  Angle     :  0.514   7.462   9185  Z= 0.261
  Chirality :  0.040   0.154    977
  Planarity :  0.003   0.037   1178
  Dihedral  :  4.516  56.460   1013
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.86 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.30), residues: 793
  helix:  1.95 (0.26), residues: 395
  sheet:  0.78 (0.80), residues: 42
  loop :  0.40 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.014   0.001   TYR B 495 
 ARG   0.003   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00276 (    7)
  link_NAG-ASN         : angle       1.96093 (   21)
  hydrogen bonds       : bond        0.04060 (  321)
  hydrogen bonds       : angle       4.38121 (  912)
  SS BOND              : bond        0.00223 (    6)
  SS BOND              : angle       0.85968 (   12)
  covalent geometry    : bond        0.00329 ( 6735)
  covalent geometry    : angle       0.50555 ( 9152)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3137.15 seconds
wall clock time: 54 minutes 55.01 seconds (3295.01 seconds total)