Starting phenix.real_space_refine
on Thu Jun  5 21:21:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sy8_25520/06_2025/7sy8_25520.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sy8_25520/06_2025/7sy8_25520.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sy8_25520/06_2025/7sy8_25520.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sy8_25520/06_2025/7sy8_25520.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sy8_25520/06_2025/7sy8_25520.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sy8_25520/06_2025/7sy8_25520.cif"
  }
  resolution = 3.14
  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=   0.029
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    4190      2.51       5
     N    1077      2.21       5
     O    1248      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-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6552
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1592
          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: {'PCIS': 1, 'PTRANS': 26, '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: 4.54, per 1000 atoms: 0.69
  Number of scatterers: 6552
  At special positions: 0
  Unit cell: (78, 83, 123, 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    1248      8.00
     N    1077      7.00
     C    4190      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=2.03
    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: 1.40
  Conformation dependent library (CDL) restraints added in 866.7 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:
      39 helices and 7 sheets defined
      58.1% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 4.272A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 388
      removed outlier: 4.320A  pdb=" N   ASN B 388 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.698A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 4.023A  pdb=" N   ASN E  33 " --> pdb=" O   LEU E  29 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   HIS E  34 " --> pdb=" O   ASP E  30 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
      removed outlier: 3.587A  pdb=" N   GLN E  81 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.723A  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 146 through 155
      removed outlier: 3.909A  pdb=" N   ILE E 151 " --> pdb=" O   GLY E 147 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.696A  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: 3.652A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.684A  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: 3.772A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 301
    Processing helix  chain 'E' and resid 303 through 319
    Processing helix  chain 'E' and resid 324 through 331
      removed outlier: 3.596A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.673A  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: 4.294A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.930A  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: 3.561A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.331A  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: 3.638A  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: 4.396A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.623A  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: 3.899A  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: 3.903A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.826A  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 131 through 132
      removed outlier: 3.749A  pdb=" N   LEU E 142 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263
      removed outlier: 6.073A  pdb=" N   LEU E 262 " --> pdb=" O   VAL E 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352
      removed outlier: 6.367A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    323 hydrogen bonds defined for protein.
    918 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: 1.66

  Time building geometry restraints manager: 1.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2077
        1.34 -     1.47: 1790
        1.47 -     1.60: 2810
        1.60 -     1.72: 0
        1.72 -     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  1.466 -0.060 2.00e-02 2.50e+03 9.15e+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 7.07e+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 6.12e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.451 -0.045 2.00e-02 2.50e+03 4.96e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.64e+00
  ... (remaining 6730 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 8817
        2.10 -     4.20: 296
        4.20 -     6.30: 31
        6.30 -     8.40: 6
        8.40 -    10.50: 4
  Bond angle restraints: 9154
  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
     122.46  127.96   -5.50 1.41e+00 5.03e-01 1.52e+01
  angle pdb=" CA  CYS E 141 "
        pdb=" CB  CYS E 141 "
        pdb=" SG  CYS E 141 "
      ideal   model   delta    sigma   weight residual
     114.40  123.33   -8.93 2.30e+00 1.89e-01 1.51e+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  120.68   -6.78 1.80e+00 3.09e-01 1.42e+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  116.25   -3.65 1.00e+00 1.00e+00 1.33e+01
  angle pdb=" CB  ARG B 457 "
        pdb=" CG  ARG B 457 "
        pdb=" CD  ARG B 457 "
      ideal   model   delta    sigma   weight residual
     111.30  118.77   -7.47 2.30e+00 1.89e-01 1.05e+01
  ... (remaining 9149 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.02: 3667
       17.02 -    34.04: 318
       34.04 -    51.06: 56
       51.06 -    68.08: 12
       68.08 -    85.09: 11
  Dihedral angle restraints: 4064
    sinusoidal: 1725
      harmonic: 2339
  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  -43.35  -42.65     1      1.00e+01 1.00e-02 2.54e+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   12.46   66.54     1      2.00e+01 2.50e-03 1.44e+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 -131.42    8.82     0      2.50e+00 1.60e-01 1.24e+01
  ... (remaining 4061 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 722
       0.057 -    0.114: 197
       0.114 -    0.171: 53
       0.171 -    0.227: 5
       0.227 -    0.284: 2
  Chirality restraints: 979
  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    2.23    0.28 2.00e-01 2.50e+01 2.02e+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   -2.37   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  VAL B 350 "
            pdb=" CA  VAL B 350 "
            pdb=" CG1 VAL B 350 "
            pdb=" CG2 VAL B 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 976 not shown)

  Planarity restraints: 1183
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE E  40 "   -0.021 2.00e-02 2.50e+03   4.18e-02 1.74e+01
        pdb=" C   PHE E  40 "    0.072 2.00e-02 2.50e+03
        pdb=" O   PHE E  40 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   TYR E  41 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.047 5.00e-02 4.00e+02   7.03e-02 7.91e+00
        pdb=" N   PRO E 590 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 499 "   -0.046 5.00e-02 4.00e+02   6.90e-02 7.62e+00
        pdb=" N   PRO E 500 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO E 500 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO E 500 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1180 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1900
        2.82 -     3.34: 5963
        3.34 -     3.86: 11272
        3.86 -     4.38: 12880
        4.38 -     4.90: 22296
  Nonbonded interactions: 54311
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OD1 ASN B 487 "
            pdb=" OH  TYR E  83 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" NH2 ARG B 454 "
            pdb=" O   SER B 469 "
     model   vdw
     2.363 3.120
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.364 3.120
  ... (remaining 54306 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:             2.610
  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:                     18.070
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
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      :  0.005   0.064   6748  Z= 0.243
  Angle     :  0.903  12.371   9187  Z= 0.498
  Chirality :  0.057   0.284    979
  Planarity :  0.007   0.070   1176
  Dihedral  : 13.429  85.095   2546
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.20 (0.26), residues: 793
  helix:  0.27 (0.23), residues: 386
  sheet:  0.94 (0.70), residues: 43
  loop : -0.60 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E  69 
 HIS   0.004   0.001   HIS E 378 
 PHE   0.028   0.003   PHE E 369 
 TYR   0.041   0.003   TYR B 495 
 ARG   0.013   0.001   ARG E 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00711 (    7)
  link_NAG-ASN         : angle       4.36532 (   21)
  hydrogen bonds       : bond        0.14338 (  323)
  hydrogen bonds       : angle       6.28296 (  918)
  SS BOND              : bond        0.00552 (    6)
  SS BOND              : angle       2.69190 (   12)
  covalent geometry    : bond        0.00520 ( 6735)
  covalent geometry    : angle       0.87490 ( 9154)

*********************** 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
  80 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8595 (m-30) cc_final: 0.8295 (m-30)
REVERT: B  471 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7987 (tm-30)
REVERT: E  149 ASN cc_start: 0.9152 (m-40) cc_final: 0.8933 (m-40)
REVERT: E  256 ILE cc_start: 0.8944 (mp) cc_final: 0.8538 (mt)
REVERT: E  455 MET cc_start: 0.8718 (tmm) cc_final: 0.8484 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.2524
  time to fit residues: 25.7719
Evaluate side-chains
  47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   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
E 154 ASN
** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 552 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.062908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.048204 restraints weight = 21985.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 3.52
r_work: 0.2699 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6748  Z= 0.182
  Angle     :  0.590   9.237   9187  Z= 0.296
  Chirality :  0.042   0.202    979
  Planarity :  0.004   0.041   1176
  Dihedral  :  5.608  51.978   1013
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.71 %
    Favored  : 92.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.28), residues: 793
  helix:  1.31 (0.25), residues: 394
  sheet:  0.85 (0.74), residues: 43
  loop : -0.24 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.021   0.001   TYR B 495 
 ARG   0.007   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00392 (    7)
  link_NAG-ASN         : angle       2.84178 (   21)
  hydrogen bonds       : bond        0.04452 (  323)
  hydrogen bonds       : angle       4.75887 (  918)
  SS BOND              : bond        0.00428 (    6)
  SS BOND              : angle       2.09642 (   12)
  covalent geometry    : bond        0.00402 ( 6735)
  covalent geometry    : angle       0.57026 ( 9154)

*********************** 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
  50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8457 (ttmm)
REVERT: B  405 ASP cc_start: 0.8966 (m-30) cc_final: 0.8691 (m-30)
REVERT: B  471 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8444 (tm-30)
REVERT: E  149 ASN cc_start: 0.9139 (m-40) cc_final: 0.8695 (m110)
REVERT: E  249 MET cc_start: 0.9259 (ttm) cc_final: 0.9021 (mtt)
REVERT: E  256 ILE cc_start: 0.8945 (mp) cc_final: 0.8549 (mt)
  outliers start: 5
  outliers final: 3
  residues processed: 50
  average time/residue: 0.2050
  time to fit residues: 14.2901
Evaluate side-chains
  46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 43
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   34 HIS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  250 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0470
   chunk 67 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0670
   chunk 66 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.5416

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

Flipped N/Q/H residues before XYZ refinement:
E 374 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.063463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.048956 restraints weight = 22118.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 3.50
r_work: 0.2717 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6748  Z= 0.112
  Angle     :  0.513   9.834   9187  Z= 0.254
  Chirality :  0.040   0.164    979
  Planarity :  0.004   0.035   1176
  Dihedral  :  4.992  54.329   1013
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  6.86 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.25 (0.29), residues: 793
  helix:  1.68 (0.26), residues: 391
  sheet:  0.72 (0.72), residues: 43
  loop : -0.04 (0.31), residues: 359

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   0.013   0.001   PHE E 369 
 TYR   0.015   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       2.29956 (   21)
  hydrogen bonds       : bond        0.03889 (  323)
  hydrogen bonds       : angle       4.48792 (  918)
  SS BOND              : bond        0.00308 (    6)
  SS BOND              : angle       1.16530 (   12)
  covalent geometry    : bond        0.00242 ( 6735)
  covalent geometry    : angle       0.49978 ( 9154)

*********************** 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
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8361 (ttmm)
REVERT: B  405 ASP cc_start: 0.8971 (m-30) cc_final: 0.8648 (m-30)
REVERT: B  471 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8499 (tm-30)
REVERT: B  484 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8863 (tptp)
REVERT: E  149 ASN cc_start: 0.9197 (m-40) cc_final: 0.8892 (m-40)
REVERT: E  249 MET cc_start: 0.9199 (ttm) cc_final: 0.8949 (mtt)
REVERT: E  256 ILE cc_start: 0.8907 (mp) cc_final: 0.8363 (mt)
REVERT: E  332 MET cc_start: 0.8716 (tmm) cc_final: 0.8484 (tmm)
  outliers start: 10
  outliers final: 6
  residues processed: 57
  average time/residue: 0.1910
  time to fit residues: 14.9321
Evaluate side-chains
  50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   34 HIS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  344 CYS
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0670
   chunk 68 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.9322

-------------------------------------------------------------------------------
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 = 0.3200 r_free = 0.3200 target = 0.062195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.047514 restraints weight = 22791.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.2813 rms_B_bonded: 3.55
r_work: 0.2676 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6748  Z= 0.150
  Angle     :  0.529  11.474   9187  Z= 0.259
  Chirality :  0.040   0.142    979
  Planarity :  0.004   0.036   1176
  Dihedral  :  4.744  55.972   1013
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  7.71 %
    Favored  : 90.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.43 (0.29), residues: 793
  helix:  1.76 (0.26), residues: 397
  sheet:  0.54 (0.71), residues: 43
  loop :  0.16 (0.32), 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   0.013   0.001   PHE E 369 
 TYR   0.014   0.001   TYR B 495 
 ARG   0.005   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00294 (    7)
  link_NAG-ASN         : angle       2.01195 (   21)
  hydrogen bonds       : bond        0.03892 (  323)
  hydrogen bonds       : angle       4.42390 (  918)
  SS BOND              : bond        0.00241 (    6)
  SS BOND              : angle       0.88573 (   12)
  covalent geometry    : bond        0.00335 ( 6735)
  covalent geometry    : angle       0.52028 ( 9154)

*********************** 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
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8961 (m-30) cc_final: 0.8559 (m-30)
REVERT: E  149 ASN cc_start: 0.9219 (m-40) cc_final: 0.8924 (m-40)
REVERT: E  249 MET cc_start: 0.9206 (ttm) cc_final: 0.8947 (mtt)
REVERT: E  256 ILE cc_start: 0.8906 (mp) cc_final: 0.8354 (mt)
  outliers start: 10
  outliers final: 6
  residues processed: 57
  average time/residue: 0.2137
  time to fit residues: 16.4919
Evaluate side-chains
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   34 HIS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  344 CYS
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 72 optimal weight:    0.6980
   chunk 30 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3217 r_free = 0.3217 target = 0.062830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.048433 restraints weight = 21948.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 3.45
r_work: 0.2713 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6748  Z= 0.131
  Angle     :  0.512  10.367   9187  Z= 0.251
  Chirality :  0.040   0.239    979
  Planarity :  0.003   0.039   1176
  Dihedral  :  4.585  57.383   1013
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.14 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.56 (0.29), residues: 793
  helix:  1.93 (0.26), residues: 391
  sheet:  0.60 (0.72), residues: 43
  loop :  0.16 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.012   0.001   PHE E 315 
 TYR   0.012   0.001   TYR B 495 
 ARG   0.005   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00279 (    7)
  link_NAG-ASN         : angle       1.82295 (   21)
  hydrogen bonds       : bond        0.03755 (  323)
  hydrogen bonds       : angle       4.35631 (  918)
  SS BOND              : bond        0.00220 (    6)
  SS BOND              : angle       0.77959 (   12)
  covalent geometry    : bond        0.00293 ( 6735)
  covalent geometry    : angle       0.50444 ( 9154)

*********************** 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
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8417 (ttmm)
REVERT: B  405 ASP cc_start: 0.8934 (m-30) cc_final: 0.8538 (m-30)
REVERT: E  140 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8664 (tm-30)
REVERT: E  149 ASN cc_start: 0.9240 (m-40) cc_final: 0.8818 (m-40)
REVERT: E  249 MET cc_start: 0.9206 (ttm) cc_final: 0.8929 (mtt)
REVERT: E  256 ILE cc_start: 0.8855 (mp) cc_final: 0.8233 (mt)
REVERT: E  332 MET cc_start: 0.8613 (tmm) cc_final: 0.8403 (tmm)
  outliers start: 9
  outliers final: 7
  residues processed: 55
  average time/residue: 0.2046
  time to fit residues: 15.4535
Evaluate side-chains
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain E residue   34 HIS
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  140 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  344 CYS
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 56 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3213 r_free = 0.3213 target = 0.062634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.048290 restraints weight = 21753.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 3.41
r_work: 0.2705 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.2472

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= 0.132
  Angle     :  0.518  12.813   9187  Z= 0.252
  Chirality :  0.040   0.203    979
  Planarity :  0.003   0.042   1176
  Dihedral  :  4.548  57.808   1013
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  9.00 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.61 (0.29), residues: 793
  helix:  1.98 (0.26), residues: 391
  sheet:  0.58 (0.74), residues: 43
  loop :  0.19 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.011   0.001   PHE E 369 
 TYR   0.012   0.001   TYR B 495 
 ARG   0.005   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00247 (    7)
  link_NAG-ASN         : angle       1.75728 (   21)
  hydrogen bonds       : bond        0.03710 (  323)
  hydrogen bonds       : angle       4.31099 (  918)
  SS BOND              : bond        0.00226 (    6)
  SS BOND              : angle       0.67277 (   12)
  covalent geometry    : bond        0.00296 ( 6735)
  covalent geometry    : angle       0.51143 ( 9154)

*********************** 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
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8409 (ttmm)
REVERT: B  405 ASP cc_start: 0.8921 (m-30) cc_final: 0.8523 (m-30)
REVERT: E  140 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8642 (tm-30)
REVERT: E  149 ASN cc_start: 0.9254 (m-40) cc_final: 0.8836 (m-40)
REVERT: E  249 MET cc_start: 0.9215 (ttm) cc_final: 0.8926 (mtt)
REVERT: E  256 ILE cc_start: 0.8865 (mp) cc_final: 0.8208 (mt)
REVERT: E  292 ASP cc_start: 0.8427 (t0) cc_final: 0.8156 (t0)
REVERT: E  332 MET cc_start: 0.8581 (tmm) cc_final: 0.8362 (tmm)
  outliers start: 11
  outliers final: 7
  residues processed: 55
  average time/residue: 0.2041
  time to fit residues: 15.4668
Evaluate side-chains
  54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   34 HIS
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  140 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  344 CYS
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    0.3980
   chunk 5 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.062242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.047727 restraints weight = 21956.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 3.44
r_work: 0.2692 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2591

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= 0.142
  Angle     :  0.517  11.926   9187  Z= 0.254
  Chirality :  0.041   0.220    979
  Planarity :  0.003   0.042   1176
  Dihedral  :  4.552  58.509   1013
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.57 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.66 (0.29), residues: 793
  helix:  2.00 (0.26), residues: 391
  sheet:  0.51 (0.74), residues: 43
  loop :  0.26 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.011   0.001   PHE E 315 
 TYR   0.011   0.001   TYR B 495 
 ARG   0.006   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00220 (    7)
  link_NAG-ASN         : angle       1.71160 (   21)
  hydrogen bonds       : bond        0.03735 (  323)
  hydrogen bonds       : angle       4.30524 (  918)
  SS BOND              : bond        0.00233 (    6)
  SS BOND              : angle       0.70852 (   12)
  covalent geometry    : bond        0.00319 ( 6735)
  covalent geometry    : angle       0.51065 ( 9154)

*********************** 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
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 LYS cc_start: 0.8848 (ttmm) cc_final: 0.8408 (ttmm)
REVERT: B  405 ASP cc_start: 0.8972 (m-30) cc_final: 0.8563 (m-30)
REVERT: E  140 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8686 (tm-30)
REVERT: E  149 ASN cc_start: 0.9280 (m-40) cc_final: 0.8888 (m-40)
REVERT: E  249 MET cc_start: 0.9224 (ttm) cc_final: 0.8920 (mtt)
REVERT: E  256 ILE cc_start: 0.8888 (mp) cc_final: 0.8228 (mt)
  outliers start: 10
  outliers final: 8
  residues processed: 59
  average time/residue: 0.1979
  time to fit residues: 16.2505
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   34 HIS
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  140 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  344 CYS
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    0.0570
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 70 optimal weight:    0.5980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.062616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.048331 restraints weight = 21889.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 3.41
r_work: 0.2708 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6748  Z= 0.119
  Angle     :  0.510  11.795   9187  Z= 0.249
  Chirality :  0.040   0.281    979
  Planarity :  0.003   0.042   1176
  Dihedral  :  4.478  58.454   1013
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.43 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: 793
  helix:  1.97 (0.26), residues: 397
  sheet:  0.70 (0.75), residues: 42
  loop :  0.28 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.010   0.001   PHE E 315 
 TYR   0.010   0.001   TYR B 495 
 ARG   0.007   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00231 (    7)
  link_NAG-ASN         : angle       1.67855 (   21)
  hydrogen bonds       : bond        0.03604 (  323)
  hydrogen bonds       : angle       4.26808 (  918)
  SS BOND              : bond        0.00220 (    6)
  SS BOND              : angle       0.66284 (   12)
  covalent geometry    : bond        0.00267 ( 6735)
  covalent geometry    : angle       0.50377 ( 9154)

*********************** 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
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8395 (ttmm)
REVERT: B  405 ASP cc_start: 0.8952 (m-30) cc_final: 0.8543 (m-30)
REVERT: E  140 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8712 (tm-30)
REVERT: E  149 ASN cc_start: 0.9281 (m-40) cc_final: 0.8873 (m-40)
REVERT: E  249 MET cc_start: 0.9230 (ttm) cc_final: 0.8924 (mtt)
REVERT: E  256 ILE cc_start: 0.8870 (mp) cc_final: 0.8527 (mp)
  outliers start: 9
  outliers final: 7
  residues processed: 58
  average time/residue: 0.2092
  time to fit residues: 16.9449
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   34 HIS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  140 GLU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  344 CYS
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
E 535 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.059147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.044510 restraints weight = 22642.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.2739 rms_B_bonded: 3.40
r_work: 0.2602 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   6748  Z= 0.300
  Angle     :  0.645  10.967   9187  Z= 0.322
  Chirality :  0.045   0.291    979
  Planarity :  0.004   0.042   1176
  Dihedral  :  5.117  59.926   1013
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.86 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.51 (0.29), residues: 793
  helix:  1.76 (0.26), residues: 389
  sheet: -0.07 (0.65), residues: 53
  loop :  0.45 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.002   PHE E 400 
 TYR   0.015   0.002   TYR E 385 
 ARG   0.006   0.001   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00312 (    7)
  link_NAG-ASN         : angle       1.97608 (   21)
  hydrogen bonds       : bond        0.04487 (  323)
  hydrogen bonds       : angle       4.61150 (  918)
  SS BOND              : bond        0.00323 (    6)
  SS BOND              : angle       1.06971 (   12)
  covalent geometry    : bond        0.00673 ( 6735)
  covalent geometry    : angle       0.63776 ( 9154)

*********************** 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
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8970 (m-30) cc_final: 0.8482 (m-30)
REVERT: E  140 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8844 (tm-30)
REVERT: E  249 MET cc_start: 0.9324 (ttm) cc_final: 0.8965 (mtt)
REVERT: E  256 ILE cc_start: 0.9056 (mp) cc_final: 0.8557 (mt)
  outliers start: 9
  outliers final: 5
  residues processed: 51
  average time/residue: 0.2060
  time to fit residues: 14.7558
Evaluate side-chains
  49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   34 HIS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  140 GLU
Chi-restraints excluded: chain E residue  344 CYS
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.061337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.046862 restraints weight = 22213.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 3.39
r_work: 0.2675 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6748  Z= 0.135
  Angle     :  0.540  11.452   9187  Z= 0.263
  Chirality :  0.041   0.299    979
  Planarity :  0.003   0.043   1176
  Dihedral  :  4.720  58.950   1013
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.14 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.62 (0.30), residues: 793
  helix:  1.82 (0.26), residues: 397
  sheet:  0.33 (0.74), residues: 43
  loop :  0.42 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.011   0.001   PHE E 315 
 TYR   0.010   0.001   TYR B 495 
 ARG   0.007   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00249 (    7)
  link_NAG-ASN         : angle       1.84797 (   21)
  hydrogen bonds       : bond        0.03789 (  323)
  hydrogen bonds       : angle       4.40592 (  918)
  SS BOND              : bond        0.00253 (    6)
  SS BOND              : angle       0.74919 (   12)
  covalent geometry    : bond        0.00304 ( 6735)
  covalent geometry    : angle       0.53320 ( 9154)

********************** 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
  54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 LYS cc_start: 0.8834 (ttmm) cc_final: 0.8446 (ttmm)
REVERT: B  405 ASP cc_start: 0.8985 (m-30) cc_final: 0.8546 (m-30)
REVERT: E  140 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8806 (tm-30)
REVERT: E  249 MET cc_start: 0.9243 (ttm) cc_final: 0.8939 (mtt)
REVERT: E  256 ILE cc_start: 0.8996 (mp) cc_final: 0.8428 (mt)
REVERT: E  474 MET cc_start: 0.9043 (mmp) cc_final: 0.8796 (mmp)
  outliers start: 7
  outliers final: 6
  residues processed: 54
  average time/residue: 0.2186
  time to fit residues: 16.3192
Evaluate side-chains
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   34 HIS
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  140 GLU
Chi-restraints excluded: chain E residue  344 CYS
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 75 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 47 optimal weight:    0.4980
   chunk 46 optimal weight:    0.5980
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3200 r_free = 0.3200 target = 0.062077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.047742 restraints weight = 22332.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.2831 rms_B_bonded: 3.41
r_work: 0.2696 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6748  Z= 0.122
  Angle     :  0.532  11.809   9187  Z= 0.258
  Chirality :  0.041   0.300    979
  Planarity :  0.003   0.043   1176
  Dihedral  :  4.518  58.698   1013
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.00 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.72 (0.30), residues: 793
  helix:  1.99 (0.26), residues: 395
  sheet:  0.53 (0.75), residues: 42
  loop :  0.35 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.010   0.001   PHE E 369 
 TYR   0.010   0.001   TYR B 495 
 ARG   0.007   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00246 (    7)
  link_NAG-ASN         : angle       1.77179 (   21)
  hydrogen bonds       : bond        0.03602 (  323)
  hydrogen bonds       : angle       4.27994 (  918)
  SS BOND              : bond        0.00222 (    6)
  SS BOND              : angle       0.62234 (   12)
  covalent geometry    : bond        0.00274 ( 6735)
  covalent geometry    : angle       0.52534 ( 9154)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3178.09 seconds
wall clock time: 55 minutes 26.76 seconds (3326.76 seconds total)