Starting phenix.real_space_refine
on Fri Aug 22 17:43:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8whz_37553/08_2025/8whz_37553.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8whz_37553/08_2025/8whz_37553.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8whz_37553/08_2025/8whz_37553.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8whz_37553/08_2025/8whz_37553.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8whz_37553/08_2025/8whz_37553.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8whz_37553/08_2025/8whz_37553.cif"
  }
  resolution = 3.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.044
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     Cl      1      4.86       5
     C    4173      2.51       5
     N    1073      2.21       5
     O    1230      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6515
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
    Chain: "B"
      Number of atoms: 1559
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1559
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 13, 'TRANS': 180}
    Chain: "A"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.44, per 1000 atoms: 0.22
  Number of scatterers: 6515
  At special positions: 0
  Unit cell: (75.97, 95.23, 114.49, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Cl      1     17.00
     S      37     16.00
     O    1230      8.00
     N    1073      7.00
     C    4173      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    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=2.03
    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=2.03

  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 A 903 " - " ASN A 546 "
      " NAG A 904 " - " ASN A  90 "
      " NAG A 905 " - " ASN A 322 "
      " NAG A 906 " - " ASN A  53 "
      " NAG B 601 " - " ASN B 354 "
      " NAG B 602 " - " ASN B 343 "
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 387.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 378 "


  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      57.1% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 52
      removed outlier: 3.795A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 81
    Processing helix  chain 'A' and resid 82 through 83
      No H-bonds generated for 'chain 'A' and resid 82 through 83'
    Processing helix  chain 'A' and resid 84 through 88
    Processing helix  chain 'A' and resid 90 through 102
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.802A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 4.312A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 218 through 252
      removed outlier: 3.752A  pdb=" N   LEU A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.918A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.743A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.685A  pdb=" N   ARG A 393 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 413
      removed outlier: 3.642A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 4.240A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 485
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.753A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.827A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.532A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'B' and resid 337 through 343
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.894A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 371
    Processing helix  chain 'B' and resid 403 through 410
      removed outlier: 3.806A  pdb=" N   SER B 408 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.788A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 3.666A  pdb=" N   THR A 347 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A 359 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.875A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453
      removed outlier: 3.523A  pdb=" N   TYR B 453 " --> pdb=" O   GLN B 493 " (cutoff:3.500A)

    315 hydrogen bonds defined for protein.
    903 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1864
        1.33 -     1.46: 1357
        1.46 -     1.58: 3422
        1.58 -     1.70: 1
        1.70 -     1.82: 58
  Bond restraints: 6702
  Sorted by residual:
  bond pdb=" C   THR A  27 "
       pdb=" N   PHE A  28 "
    ideal  model  delta    sigma   weight residual
    1.335  1.292  0.043 1.30e-02 5.92e+03 1.12e+01
  bond pdb=" N   THR A  27 "
       pdb=" CA  THR A  27 "
    ideal  model  delta    sigma   weight residual
    1.459  1.421  0.038 1.17e-02 7.31e+03 1.08e+01
  bond pdb=" CA  ARG B 457 "
       pdb=" CB  ARG B 457 "
    ideal  model  delta    sigma   weight residual
    1.534  1.480  0.053 1.78e-02 3.16e+03 8.94e+00
  bond pdb=" CA  THR A  27 "
       pdb=" C   THR A  27 "
    ideal  model  delta    sigma   weight residual
    1.524  1.492  0.032 1.24e-02 6.50e+03 6.85e+00
  bond pdb=" CB  PRO B 384 "
       pdb=" CG  PRO B 384 "
    ideal  model  delta    sigma   weight residual
    1.492  1.583 -0.091 5.00e-02 4.00e+02 3.30e+00
  ... (remaining 6697 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 8753
        1.88 -     3.77: 312
        3.77 -     5.65: 37
        5.65 -     7.54: 6
        7.54 -     9.42: 2
  Bond angle restraints: 9110
  Sorted by residual:
  angle pdb=" N   LYS A 313 "
        pdb=" CA  LYS A 313 "
        pdb=" C   LYS A 313 "
      ideal   model   delta    sigma   weight residual
     111.82  106.74    5.08 1.16e+00 7.43e-01 1.92e+01
  angle pdb=" CA  PRO B 384 "
        pdb=" N   PRO B 384 "
        pdb=" CD  PRO B 384 "
      ideal   model   delta    sigma   weight residual
     112.00  106.33    5.67 1.40e+00 5.10e-01 1.64e+01
  angle pdb=" N   CYS A 498 "
        pdb=" CA  CYS A 498 "
        pdb=" C   CYS A 498 "
      ideal   model   delta    sigma   weight residual
     110.44  105.84    4.60 1.20e+00 6.94e-01 1.47e+01
  angle pdb=" CA  ARG B 457 "
        pdb=" C   ARG B 457 "
        pdb=" N   LYS B 458 "
      ideal   model   delta    sigma   weight residual
     115.61  120.89   -5.28 1.45e+00 4.76e-01 1.32e+01
  angle pdb=" N   VAL A 364 "
        pdb=" CA  VAL A 364 "
        pdb=" C   VAL A 364 "
      ideal   model   delta    sigma   weight residual
     106.21  109.67   -3.46 1.07e+00 8.73e-01 1.05e+01
  ... (remaining 9105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3628
       17.95 -    35.90: 318
       35.90 -    53.85: 58
       53.85 -    71.80: 17
       71.80 -    89.75: 8
  Dihedral angle restraints: 4029
    sinusoidal: 1705
      harmonic: 2324
  Sorted by residual:
  dihedral pdb=" CA  CYS B 361 "
           pdb=" C   CYS B 361 "
           pdb=" N   VAL B 362 "
           pdb=" CA  VAL B 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.36   36.64     0      5.00e+00 4.00e-02 5.37e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.85  -41.85     1      1.00e+01 1.00e-02 2.45e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  129.35  -36.35     1      1.00e+01 1.00e-02 1.87e+01
  ... (remaining 4026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 705
       0.049 -    0.097: 202
       0.097 -    0.146: 54
       0.146 -    0.194: 2
       0.194 -    0.243: 1
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" C1  NAG A 905 "
            pdb=" ND2 ASN A 322 "
            pdb=" C2  NAG A 905 "
            pdb=" O5  NAG A 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  PRO B 384 "
            pdb=" N   PRO B 384 "
            pdb=" C   PRO B 384 "
            pdb=" CB  PRO B 384 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.19 2.00e-01 2.50e+01 9.37e-01
  chirality pdb=" CG  LEU B 492 "
            pdb=" CB  LEU B 492 "
            pdb=" CD1 LEU B 492 "
            pdb=" CD2 LEU B 492 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.83e-01
  ... (remaining 961 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 383 "   -0.072 5.00e-02 4.00e+02   1.05e-01 1.78e+01
        pdb=" N   PRO B 384 "    0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO B 384 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO B 384 "   -0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  69 "   -0.016 2.00e-02 2.50e+03   1.13e-02 3.22e+00
        pdb=" CG  TRP A  69 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  69 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  69 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  69 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  69 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  69 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  69 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  69 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  69 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 506 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO B 507 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 507 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 507 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.48: 45
        2.48 -     3.08: 4740
        3.08 -     3.69: 10301
        3.69 -     4.29: 14541
        4.29 -     4.90: 22781
  Nonbonded interactions: 52408
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 421 "
            pdb=" CZ  ARG B 457 "
     model   vdw
     1.873 3.270
  nonbonded pdb=" O   TYR B 421 "
            pdb=" NH1 ARG B 457 "
     model   vdw
     1.994 3.120
  nonbonded pdb=" NH2 ARG B 454 "
            pdb=" CG  ARG B 457 "
     model   vdw
     2.068 3.520
  nonbonded pdb=" O   LEU A 156 "
            pdb=" OH  TYR A 252 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" CZ  ARG B 454 "
            pdb=" NE  ARG B 457 "
     model   vdw
     2.171 3.350
  ... (remaining 52403 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 group one per residue
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:             2.560
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.130
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
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      :  0.004   0.091   6717  Z= 0.208
  Angle     :  0.801   9.421   9142  Z= 0.458
  Chirality :  0.047   0.243    964
  Planarity :  0.006   0.105   1172
  Dihedral  : 14.476  89.752   2516
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.07 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.29 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.30), residues: 787
  helix:  0.61 (0.26), residues: 390
  sheet: -0.55 (0.89), residues: 35
  loop : -1.43 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 582 
 TYR   0.020   0.002   TYR A 454 
 PHE   0.014   0.002   PHE A 230 
 TRP   0.030   0.002   TRP A  69 
 HIS   0.004   0.001   HIS A 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 6702)
  covalent geometry    : angle       0.79127 ( 9110)
  SS BOND              : bond        0.00183 (    7)
  SS BOND              : angle       1.52970 (   14)
  hydrogen bonds       : bond        0.15190 (  315)
  hydrogen bonds       : angle       6.20077 (  903)
  metal coordination   : bond        0.00062 (    2)
  link_NAG-ASN         : bond        0.00435 (    6)
  link_NAG-ASN         : angle       2.70915 (   18)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 201
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.6456 (mtp) cc_final: 0.6173 (mmm)
REVERT: A  243 TYR cc_start: 0.9040 (t80) cc_final: 0.8645 (t80)
REVERT: A  270 MET cc_start: 0.7170 (tpt) cc_final: 0.6919 (tpt)
REVERT: A  333 LEU cc_start: 0.9346 (mt) cc_final: 0.9133 (mm)
REVERT: A  408 MET cc_start: 0.8318 (mmp) cc_final: 0.8081 (mmt)
REVERT: A  461 TRP cc_start: 0.8963 (m-10) cc_final: 0.8734 (m-10)
REVERT: A  484 ILE cc_start: 0.8728 (mm) cc_final: 0.8256 (tp)
REVERT: B  406 GLU cc_start: 0.8224 (mp0) cc_final: 0.8014 (mp0)
  outliers start: 2
  outliers final: 1
  residues processed: 202
  average time/residue: 0.0889
  time to fit residues: 23.1837
Evaluate side-chains
  126 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A  58 ASN
A  60 GLN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 GLN
B 417 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 505 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.143034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.114476 restraints weight = 16213.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.117845 restraints weight = 8946.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.120329 restraints weight = 6052.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.121684 restraints weight = 4617.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.122963 restraints weight = 3892.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6717  Z= 0.188
  Angle     :  0.711   8.190   9142  Z= 0.369
  Chirality :  0.046   0.223    964
  Planarity :  0.005   0.053   1172
  Dihedral  :  6.100  52.070    985
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.81 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 11.08 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.29), residues: 787
  helix:  0.64 (0.25), residues: 406
  sheet: -0.35 (0.79), residues: 42
  loop : -1.24 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 582 
 TYR   0.019   0.002   TYR B 421 
 PHE   0.034   0.003   PHE B 375 
 TRP   0.022   0.002   TRP A 165 
 HIS   0.005   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 6702)
  covalent geometry    : angle       0.69701 ( 9110)
  SS BOND              : bond        0.00140 (    7)
  SS BOND              : angle       1.53704 (   14)
  hydrogen bonds       : bond        0.05179 (  315)
  hydrogen bonds       : angle       5.03751 (  903)
  metal coordination   : bond        0.00089 (    2)
  link_NAG-ASN         : bond        0.00421 (    6)
  link_NAG-ASN         : angle       3.02293 (   18)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LEU cc_start: 0.8319 (mt) cc_final: 0.7875 (mm)
REVERT: A  243 TYR cc_start: 0.8866 (t80) cc_final: 0.8654 (t80)
REVERT: A  323 MET cc_start: 0.8276 (mmt) cc_final: 0.7266 (mmm)
REVERT: A  360 MET cc_start: 0.8343 (ppp) cc_final: 0.7710 (ppp)
REVERT: A  594 TRP cc_start: 0.8075 (t-100) cc_final: 0.7843 (t-100)
REVERT: B  347 PHE cc_start: 0.6372 (m-80) cc_final: 0.5932 (m-80)
REVERT: B  369 TYR cc_start: 0.6799 (m-80) cc_final: 0.6585 (m-80)
  outliers start: 18
  outliers final: 9
  residues processed: 141
  average time/residue: 0.0731
  time to fit residues: 13.8513
Evaluate side-chains
  114 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 ASN
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  453 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0570
   chunk 11 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 23 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    0.8700

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A  64 ASN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 GLN
A 472 GLN
A 508 ASN
B 417 ASN
B 493 GLN
B 505 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.141414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.112979 restraints weight = 15969.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.116322 restraints weight = 8964.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.118284 restraints weight = 6122.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.120001 restraints weight = 4812.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.120859 restraints weight = 4016.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.4514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6717  Z= 0.162
  Angle     :  0.661   6.882   9142  Z= 0.345
  Chirality :  0.045   0.210    964
  Planarity :  0.005   0.050   1172
  Dihedral  :  5.865  48.817    984
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.94 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.10 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.29), residues: 787
  helix:  0.62 (0.25), residues: 406
  sheet:  0.23 (0.83), residues: 42
  loop : -1.25 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 582 
 TYR   0.018   0.002   TYR A 237 
 PHE   0.019   0.002   PHE A 369 
 TRP   0.018   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 6702)
  covalent geometry    : angle       0.64877 ( 9110)
  SS BOND              : bond        0.00147 (    7)
  SS BOND              : angle       1.65196 (   14)
  hydrogen bonds       : bond        0.05036 (  315)
  hydrogen bonds       : angle       4.91443 (  903)
  metal coordination   : bond        0.00156 (    2)
  link_NAG-ASN         : bond        0.00291 (    6)
  link_NAG-ASN         : angle       2.58635 (   18)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LEU cc_start: 0.8186 (mt) cc_final: 0.7830 (mt)
REVERT: A  180 TYR cc_start: 0.7905 (m-80) cc_final: 0.7376 (m-10)
REVERT: A  243 TYR cc_start: 0.8789 (t80) cc_final: 0.8557 (t80)
REVERT: A  287 GLN cc_start: 0.6808 (OUTLIER) cc_final: 0.6280 (pm20)
REVERT: A  323 MET cc_start: 0.8377 (mmt) cc_final: 0.7140 (mmm)
REVERT: A  333 LEU cc_start: 0.9006 (mt) cc_final: 0.8723 (mm)
REVERT: A  366 MET cc_start: 0.8873 (ppp) cc_final: 0.7960 (ppp)
REVERT: A  376 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7749 (tpt)
REVERT: A  472 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7419 (pm20)
REVERT: B  369 TYR cc_start: 0.6823 (m-80) cc_final: 0.6621 (m-80)
  outliers start: 20
  outliers final: 11
  residues processed: 129
  average time/residue: 0.0742
  time to fit residues: 12.7305
Evaluate side-chains
  115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  472 GLN
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  453 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0970
   chunk 11 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 250 ASN
** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 HIS
A 472 GLN
A 508 ASN
A 598 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 505 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.140433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.112470 restraints weight = 16328.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.115719 restraints weight = 9106.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.118000 restraints weight = 6190.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.119485 restraints weight = 4762.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.120270 restraints weight = 3984.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.5152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6717  Z= 0.139
  Angle     :  0.622   6.666   9142  Z= 0.325
  Chirality :  0.044   0.207    964
  Planarity :  0.005   0.047   1172
  Dihedral  :  5.543  40.543    984
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.43 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.12 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.29), residues: 787
  helix:  0.82 (0.25), residues: 401
  sheet:  0.91 (0.82), residues: 40
  loop : -1.24 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 457 
 TYR   0.014   0.001   TYR A 237 
 PHE   0.029   0.002   PHE B 375 
 TRP   0.027   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6702)
  covalent geometry    : angle       0.61170 ( 9110)
  SS BOND              : bond        0.00262 (    7)
  SS BOND              : angle       1.70447 (   14)
  hydrogen bonds       : bond        0.04733 (  315)
  hydrogen bonds       : angle       4.73652 (  903)
  metal coordination   : bond        0.00077 (    2)
  link_NAG-ASN         : bond        0.00250 (    6)
  link_NAG-ASN         : angle       2.23778 (   18)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7405 (mmm) cc_final: 0.7185 (mmt)
REVERT: A  249 MET cc_start: 0.8235 (mtp) cc_final: 0.7344 (mpp)
REVERT: A  366 MET cc_start: 0.8844 (ppp) cc_final: 0.7934 (ppp)
REVERT: A  406 GLU cc_start: 0.8445 (tp30) cc_final: 0.8238 (mm-30)
REVERT: A  441 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8397 (ttpp)
REVERT: A  452 PHE cc_start: 0.8490 (t80) cc_final: 0.8257 (t80)
REVERT: A  467 GLU cc_start: 0.8288 (pm20) cc_final: 0.7839 (pm20)
REVERT: B  347 PHE cc_start: 0.6119 (m-80) cc_final: 0.5890 (m-10)
REVERT: B  349 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8122 (p)
REVERT: B  406 GLU cc_start: 0.7846 (mp0) cc_final: 0.7536 (mp0)
  outliers start: 19
  outliers final: 11
  residues processed: 126
  average time/residue: 0.0685
  time to fit residues: 11.7897
Evaluate side-chains
  108 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 GLN
A 378 HIS
A 380 GLN
A 472 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.138215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.110017 restraints weight = 16402.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.113231 restraints weight = 9046.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.115402 restraints weight = 6120.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.116759 restraints weight = 4737.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.117787 restraints weight = 4006.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.5738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.851   6717  Z= 0.382
  Angle     :  0.630   8.833   9142  Z= 0.333
  Chirality :  0.044   0.201    964
  Planarity :  0.005   0.045   1172
  Dihedral  :  5.444  38.748    984
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.07 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 17.84 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.28), residues: 787
  helix:  0.85 (0.25), residues: 400
  sheet:  0.45 (0.79), residues: 42
  loop : -1.33 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 219 
 TYR   0.022   0.002   TYR A 243 
 PHE   0.017   0.002   PHE B 490 
 TRP   0.030   0.002   TRP A 473 
 HIS   0.004   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6702)
  covalent geometry    : angle       0.62200 ( 9110)
  SS BOND              : bond        0.00906 (    7)
  SS BOND              : angle       1.34156 (   14)
  hydrogen bonds       : bond        0.04796 (  315)
  hydrogen bonds       : angle       4.70679 (  903)
  metal coordination   : bond        0.60174 (    2)
  link_NAG-ASN         : bond        0.00176 (    6)
  link_NAG-ASN         : angle       2.08636 (   18)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 TRP cc_start: 0.8300 (t-100) cc_final: 0.7891 (t60)
REVERT: A  287 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6478 (pm20)
REVERT: A  323 MET cc_start: 0.8453 (mmm) cc_final: 0.7065 (mmm)
REVERT: A  366 MET cc_start: 0.8883 (ppp) cc_final: 0.7926 (ppp)
REVERT: A  376 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7703 (tpt)
REVERT: A  441 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8451 (ttpp)
REVERT: B  406 GLU cc_start: 0.7997 (mp0) cc_final: 0.7584 (mp0)
  outliers start: 26
  outliers final: 17
  residues processed: 125
  average time/residue: 0.0574
  time to fit residues: 10.0330
Evaluate side-chains
  116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0870
   chunk 63 optimal weight:    0.0470
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 GLN
** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 GLN
B 439 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.138942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.111532 restraints weight = 16226.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.114758 restraints weight = 9034.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.116975 restraints weight = 6104.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.118318 restraints weight = 4680.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.119304 restraints weight = 3938.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.6037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6717  Z= 0.134
  Angle     :  0.620   6.652   9142  Z= 0.328
  Chirality :  0.044   0.198    964
  Planarity :  0.005   0.052   1172
  Dihedral  :  5.138  37.751    984
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.56 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 20.29 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.29), residues: 787
  helix:  0.90 (0.25), residues: 403
  sheet:  0.64 (0.79), residues: 40
  loop : -1.34 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 457 
 TYR   0.022   0.002   TYR A 243 
 PHE   0.031   0.001   PHE B 375 
 TRP   0.040   0.002   TRP A 473 
 HIS   0.006   0.001   HIS A 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6702)
  covalent geometry    : angle       0.61058 ( 9110)
  SS BOND              : bond        0.00637 (    7)
  SS BOND              : angle       1.98141 (   14)
  hydrogen bonds       : bond        0.04587 (  315)
  hydrogen bonds       : angle       4.60635 (  903)
  metal coordination   : bond        0.00832 (    2)
  link_NAG-ASN         : bond        0.00197 (    6)
  link_NAG-ASN         : angle       1.88086 (   18)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7083 (mmt) cc_final: 0.6674 (mmm)
REVERT: A  287 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6467 (pm20)
REVERT: A  323 MET cc_start: 0.8408 (mmm) cc_final: 0.6941 (mmm)
REVERT: A  366 MET cc_start: 0.8871 (ppp) cc_final: 0.8089 (ppp)
REVERT: A  376 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7689 (tpt)
REVERT: A  406 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8524 (mm-30)
REVERT: A  441 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8447 (ttpp)
REVERT: B  406 GLU cc_start: 0.7879 (mp0) cc_final: 0.7604 (mp0)
  outliers start: 25
  outliers final: 16
  residues processed: 120
  average time/residue: 0.0633
  time to fit residues: 10.6223
Evaluate side-chains
  116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 65 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.131779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.104197 restraints weight = 15732.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.107181 restraints weight = 8882.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.109230 restraints weight = 6058.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.110461 restraints weight = 4675.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.111398 restraints weight = 3941.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.6664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6717  Z= 0.220
  Angle     :  0.709  13.530   9142  Z= 0.373
  Chirality :  0.046   0.187    964
  Planarity :  0.005   0.053   1172
  Dihedral  :  5.910  41.654    984
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.70 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 20.00 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.29), residues: 787
  helix:  0.68 (0.25), residues: 412
  sheet:  0.29 (0.77), residues: 42
  loop : -1.42 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 482 
 TYR   0.023   0.002   TYR B 351 
 PHE   0.023   0.002   PHE A 369 
 TRP   0.036   0.002   TRP A 594 
 HIS   0.006   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 6702)
  covalent geometry    : angle       0.69957 ( 9110)
  SS BOND              : bond        0.00318 (    7)
  SS BOND              : angle       1.84199 (   14)
  hydrogen bonds       : bond        0.05470 (  315)
  hydrogen bonds       : angle       4.88625 (  903)
  metal coordination   : bond        0.00286 (    2)
  link_NAG-ASN         : bond        0.00334 (    6)
  link_NAG-ASN         : angle       2.18743 (   18)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8029 (ppp) cc_final: 0.7518 (ppp)
REVERT: A  249 MET cc_start: 0.8157 (mtp) cc_final: 0.7194 (mpp)
REVERT: A  306 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.8224 (ttp-170)
REVERT: A  323 MET cc_start: 0.8553 (mmm) cc_final: 0.7353 (mmm)
REVERT: A  366 MET cc_start: 0.9007 (ppp) cc_final: 0.8320 (ppp)
REVERT: A  376 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7760 (tpt)
REVERT: A  441 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8540 (ttpp)
REVERT: A  560 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8893 (mt)
REVERT: B  361 CYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6256 (t)
  outliers start: 32
  outliers final: 20
  residues processed: 127
  average time/residue: 0.0672
  time to fit residues: 11.8249
Evaluate side-chains
  121 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  361 CYS
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 47 optimal weight:    6.9990
   chunk 67 optimal weight:    0.2980
   chunk 4 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 GLN
A 472 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.135882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.108709 restraints weight = 16198.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.111786 restraints weight = 9090.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.113896 restraints weight = 6206.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.115040 restraints weight = 4785.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.116104 restraints weight = 4063.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.6943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6717  Z= 0.146
  Angle     :  0.661   8.375   9142  Z= 0.344
  Chirality :  0.044   0.194    964
  Planarity :  0.004   0.047   1172
  Dihedral  :  5.344  39.650    984
  Min Nonbonded Distance : 1.806

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.30 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.16 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.29), residues: 787
  helix:  0.90 (0.26), residues: 403
  sheet:  0.56 (0.77), residues: 41
  loop : -1.37 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 457 
 TYR   0.026   0.002   TYR A 243 
 PHE   0.032   0.002   PHE B 375 
 TRP   0.028   0.002   TRP A 594 
 HIS   0.004   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6702)
  covalent geometry    : angle       0.65529 ( 9110)
  SS BOND              : bond        0.00337 (    7)
  SS BOND              : angle       1.47272 (   14)
  hydrogen bonds       : bond        0.04727 (  315)
  hydrogen bonds       : angle       4.65099 (  903)
  metal coordination   : bond        0.00083 (    2)
  link_NAG-ASN         : bond        0.00164 (    6)
  link_NAG-ASN         : angle       1.74203 (   18)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7876 (ppp) cc_final: 0.7456 (ppp)
REVERT: A  121 ASN cc_start: 0.8999 (m110) cc_final: 0.8675 (m-40)
REVERT: A  234 LYS cc_start: 0.9391 (ptmm) cc_final: 0.9130 (pttp)
REVERT: A  287 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6781 (pm20)
REVERT: A  306 ARG cc_start: 0.8365 (ttp-170) cc_final: 0.8123 (ttp-170)
REVERT: A  323 MET cc_start: 0.8377 (mmm) cc_final: 0.7022 (mmm)
REVERT: A  366 MET cc_start: 0.8804 (ppp) cc_final: 0.8026 (ppp)
REVERT: A  376 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7790 (tpt)
REVERT: A  441 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8641 (ttpp)
REVERT: A  461 TRP cc_start: 0.9036 (m-10) cc_final: 0.8734 (m-10)
REVERT: A  480 MET cc_start: 0.8724 (mtt) cc_final: 0.8424 (mtm)
REVERT: A  560 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8964 (mt)
  outliers start: 23
  outliers final: 14
  residues processed: 126
  average time/residue: 0.0717
  time to fit residues: 12.1503
Evaluate side-chains
  114 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0770
   chunk 36 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.134856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.107928 restraints weight = 15625.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.110999 restraints weight = 8662.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.112998 restraints weight = 5834.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.114417 restraints weight = 4479.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.115229 restraints weight = 3722.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.7145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6717  Z= 0.144
  Angle     :  0.668   7.321   9142  Z= 0.346
  Chirality :  0.044   0.189    964
  Planarity :  0.004   0.047   1172
  Dihedral  :  5.277  38.673    984
  Min Nonbonded Distance : 1.812

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.81 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 24.03 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.29), residues: 787
  helix:  0.85 (0.25), residues: 401
  sheet:  0.35 (0.79), residues: 43
  loop : -1.29 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 457 
 TYR   0.028   0.002   TYR A 243 
 PHE   0.022   0.001   PHE A 428 
 TRP   0.025   0.002   TRP A 594 
 HIS   0.005   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6702)
  covalent geometry    : angle       0.66232 ( 9110)
  SS BOND              : bond        0.00332 (    7)
  SS BOND              : angle       1.26092 (   14)
  hydrogen bonds       : bond        0.04706 (  315)
  hydrogen bonds       : angle       4.64759 (  903)
  metal coordination   : bond        0.00090 (    2)
  link_NAG-ASN         : bond        0.00187 (    6)
  link_NAG-ASN         : angle       1.77630 (   18)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7938 (ppp) cc_final: 0.7612 (ppp)
REVERT: A  121 ASN cc_start: 0.9025 (m110) cc_final: 0.8701 (m-40)
REVERT: A  234 LYS cc_start: 0.9424 (ptmm) cc_final: 0.9107 (pttp)
REVERT: A  306 ARG cc_start: 0.8421 (ttp-170) cc_final: 0.8137 (ttp-170)
REVERT: A  323 MET cc_start: 0.8387 (mmm) cc_final: 0.7058 (mmm)
REVERT: A  366 MET cc_start: 0.8808 (ppp) cc_final: 0.8006 (ppp)
REVERT: A  376 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7691 (tpt)
REVERT: A  441 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8623 (ttpp)
REVERT: A  461 TRP cc_start: 0.9058 (m-10) cc_final: 0.8778 (m-10)
REVERT: A  560 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8950 (mt)
  outliers start: 18
  outliers final: 13
  residues processed: 115
  average time/residue: 0.0653
  time to fit residues: 10.4564
Evaluate side-chains
  116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0050
   chunk 35 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 GLN
A 472 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.136774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.109957 restraints weight = 15927.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.113026 restraints weight = 8965.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.115122 restraints weight = 6077.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.116370 restraints weight = 4669.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.117177 restraints weight = 3922.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.7317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6717  Z= 0.136
  Angle     :  0.676   7.595   9142  Z= 0.350
  Chirality :  0.045   0.186    964
  Planarity :  0.004   0.048   1172
  Dihedral  :  5.127  37.191    984
  Min Nonbonded Distance : 1.775

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.68 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.88 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.30), residues: 787
  helix:  1.05 (0.26), residues: 398
  sheet:  0.90 (0.80), residues: 41
  loop : -1.22 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 192 
 TYR   0.028   0.001   TYR A 243 
 PHE   0.021   0.001   PHE A 428 
 TRP   0.024   0.002   TRP A 594 
 HIS   0.005   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6702)
  covalent geometry    : angle       0.67215 ( 9110)
  SS BOND              : bond        0.00331 (    7)
  SS BOND              : angle       1.11584 (   14)
  hydrogen bonds       : bond        0.04528 (  315)
  hydrogen bonds       : angle       4.67341 (  903)
  metal coordination   : bond        0.00128 (    2)
  link_NAG-ASN         : bond        0.00166 (    6)
  link_NAG-ASN         : angle       1.64372 (   18)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7905 (ppp) cc_final: 0.7640 (ppp)
REVERT: A  121 ASN cc_start: 0.9015 (m110) cc_final: 0.8689 (m-40)
REVERT: A  152 MET cc_start: 0.6988 (mmt) cc_final: 0.6553 (mmm)
REVERT: A  234 LYS cc_start: 0.9433 (ptmm) cc_final: 0.9142 (pttp)
REVERT: A  249 MET cc_start: 0.8036 (mtp) cc_final: 0.7013 (mpp)
REVERT: A  280 SER cc_start: 0.8864 (m) cc_final: 0.8644 (p)
REVERT: A  287 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7082 (pm20)
REVERT: A  306 ARG cc_start: 0.8436 (ttp-170) cc_final: 0.8152 (ttp-170)
REVERT: A  323 MET cc_start: 0.8352 (mmm) cc_final: 0.6975 (mmm)
REVERT: A  366 MET cc_start: 0.8765 (ppp) cc_final: 0.7984 (ppp)
REVERT: A  376 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7673 (tpt)
REVERT: A  461 TRP cc_start: 0.9084 (m-10) cc_final: 0.8777 (m-10)
REVERT: A  467 GLU cc_start: 0.8380 (pm20) cc_final: 0.8112 (pm20)
REVERT: A  512 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8288 (t80)
  outliers start: 20
  outliers final: 13
  residues processed: 119
  average time/residue: 0.0661
  time to fit residues: 10.9908
Evaluate side-chains
  118 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 14 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 GLN
A 442 GLN
A 472 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.135148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.107784 restraints weight = 15994.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.110925 restraints weight = 8943.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.112985 restraints weight = 6047.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.114290 restraints weight = 4640.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.115265 restraints weight = 3890.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.7489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6717  Z= 0.156
  Angle     :  0.695   9.506   9142  Z= 0.361
  Chirality :  0.045   0.182    964
  Planarity :  0.004   0.047   1172
  Dihedral  :  5.217  37.333    984
  Min Nonbonded Distance : 1.744

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.07 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.88 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.30), residues: 787
  helix:  1.08 (0.26), residues: 395
  sheet:  0.47 (0.80), residues: 43
  loop : -1.15 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 357 
 TYR   0.034   0.002   TYR A 243 
 PHE   0.022   0.002   PHE A 428 
 TRP   0.023   0.002   TRP A 594 
 HIS   0.005   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6702)
  covalent geometry    : angle       0.68966 ( 9110)
  SS BOND              : bond        0.00322 (    7)
  SS BOND              : angle       1.25359 (   14)
  hydrogen bonds       : bond        0.04692 (  315)
  hydrogen bonds       : angle       4.75387 (  903)
  metal coordination   : bond        0.00127 (    2)
  link_NAG-ASN         : bond        0.00180 (    6)
  link_NAG-ASN         : angle       1.75998 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1275.70 seconds
wall clock time: 22 minutes 38.94 seconds (1358.94 seconds total)