Starting phenix.real_space_refine
on Sat May 10 16:14:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8whz_37553/05_2025/8whz_37553.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8whz_37553/05_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_37553/05_2025/8whz_37553.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8whz_37553/05_2025/8whz_37553.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8whz_37553/05_2025/8whz_37553.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8whz_37553/05_2025/8whz_37553.cif"
  }
  resolution = 3.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.044
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.34, per 1000 atoms: 0.67
  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: 1.74
  Conformation dependent library (CDL) restraints added in 910.1 milliseconds
  
  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: 0.66
  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: 1.61

  Time building geometry restraints manager: 1.99 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:             3.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.350
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.960
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (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
 TRP   0.030   0.002   TRP A  69 
 HIS   0.004   0.001   HIS A 493 
 PHE   0.014   0.002   PHE A 230 
 TYR   0.020   0.002   TYR A 454 
 ARG   0.006   0.001   ARG A 582 

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

*********************** 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  : 0.702 
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: symmetry clash
REVERT: A  152 MET cc_start: 0.6456 (mtp) cc_final: 0.6177 (mmm)
REVERT: A  243 TYR cc_start: 0.9040 (t80) cc_final: 0.8669 (t80)
REVERT: A  270 MET cc_start: 0.7170 (tpt) cc_final: 0.6916 (tpt)
REVERT: A  333 LEU cc_start: 0.9346 (mt) cc_final: 0.9130 (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: 0.8732 (m-10)
REVERT: A  484 ILE cc_start: 0.8728 (mm) cc_final: 0.8257 (tp)
REVERT: B  406 GLU cc_start: 0.8224 (mp0) cc_final: 0.8015 (mp0)
  outliers start: 2
  outliers final: 1
  residues processed: 202
  average time/residue: 0.2171
  time to fit residues: 55.9070
Evaluate side-chains
  124 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
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 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.3980
   chunk 32 optimal weight:    0.0870
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    0.2980
   overall best weight:    0.9562

-------------------------------------------------------------------------------
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 505 HIS
** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.143096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.114732 restraints weight = 16059.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.118178 restraints weight = 8978.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.120560 restraints weight = 6105.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.3723

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= 0.182
  Angle     :  0.713   8.078   9142  Z= 0.368
  Chirality :  0.047   0.219    964
  Planarity :  0.006   0.054   1172
  Dihedral  :  6.087  51.790    985
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.68 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 10.79 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.29), residues: 787
  helix:  0.59 (0.25), residues: 406
  sheet: -0.42 (0.80), residues: 42
  loop : -1.28 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 165 
 HIS   0.005   0.001   HIS A 417 
 PHE   0.034   0.003   PHE B 375 
 TYR   0.022   0.002   TYR B 421 
 ARG   0.009   0.001   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00418 (    6)
  link_NAG-ASN         : angle       3.05772 (   18)
  hydrogen bonds       : bond        0.05108 (  315)
  hydrogen bonds       : angle       5.00033 (  903)
  metal coordination   : bond        0.00150 (    2)
  SS BOND              : bond        0.00275 (    7)
  SS BOND              : angle       1.63187 (   14)
  covalent geometry    : bond        0.00408 ( 6702)
  covalent geometry    : angle       0.69820 ( 9110)

*********************** 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
  151 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  243 TYR cc_start: 0.8920 (t80) cc_final: 0.8691 (t80)
REVERT: A  323 MET cc_start: 0.8297 (mmt) cc_final: 0.7260 (mmm)
REVERT: A  360 MET cc_start: 0.8384 (ppp) cc_final: 0.8033 (ppp)
REVERT: A  366 MET cc_start: 0.8707 (ppp) cc_final: 0.7920 (ppp)
REVERT: A  467 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7078 (tm-30)
REVERT: A  468 ILE cc_start: 0.8686 (mm) cc_final: 0.7949 (mm)
REVERT: A  473 TRP cc_start: 0.7429 (m-10) cc_final: 0.7149 (m-10)
REVERT: A  480 MET cc_start: 0.8738 (mtm) cc_final: 0.8529 (mtp)
REVERT: A  557 MET cc_start: 0.8462 (tmm) cc_final: 0.8162 (ttp)
REVERT: B  347 PHE cc_start: 0.6218 (m-80) cc_final: 0.5789 (m-80)
REVERT: B  349 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8140 (p)
  outliers start: 19
  outliers final: 8
  residues processed: 142
  average time/residue: 0.1854
  time to fit residues: 35.2331
Evaluate side-chains
  115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
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  385 THR
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 47 optimal weight:    9.9990
   chunk 60 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 58 optimal weight:    0.3980
   chunk 32 optimal weight:    0.0770
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 HIS
B 417 ASN
B 493 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.143272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.114697 restraints weight = 16061.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.118265 restraints weight = 8973.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.120652 restraints weight = 6060.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.4413

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= 0.137
  Angle     :  0.640   9.111   9142  Z= 0.330
  Chirality :  0.044   0.213    964
  Planarity :  0.005   0.048   1172
  Dihedral  :  5.591  47.013    984
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.68 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.68 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.29), residues: 787
  helix:  0.67 (0.25), residues: 406
  sheet:  0.21 (0.83), residues: 42
  loop : -1.20 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.017   0.001   PHE A 369 
 TYR   0.015   0.001   TYR A 237 
 ARG   0.003   0.001   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00339 (    6)
  link_NAG-ASN         : angle       2.45365 (   18)
  hydrogen bonds       : bond        0.04678 (  315)
  hydrogen bonds       : angle       4.80849 (  903)
  metal coordination   : bond        0.00107 (    2)
  SS BOND              : bond        0.00176 (    7)
  SS BOND              : angle       1.42826 (   14)
  covalent geometry    : bond        0.00305 ( 6702)
  covalent geometry    : angle       0.62957 ( 9110)

*********************** 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
  133 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 LEU cc_start: 0.7929 (mm) cc_final: 0.7057 (mm)
REVERT: A  243 TYR cc_start: 0.8842 (t80) cc_final: 0.8625 (t80)
REVERT: A  323 MET cc_start: 0.8410 (mmt) cc_final: 0.7077 (mmm)
REVERT: A  366 MET cc_start: 0.8571 (ppp) cc_final: 0.7914 (ppp)
REVERT: A  376 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7828 (tpt)
REVERT: A  423 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8550 (tt)
REVERT: A  441 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8414 (ttpp)
REVERT: A  467 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7032 (tm-30)
REVERT: A  468 ILE cc_start: 0.8530 (mm) cc_final: 0.7601 (mm)
REVERT: B  340 GLU cc_start: 0.6909 (mp0) cc_final: 0.6541 (mp0)
REVERT: B  347 PHE cc_start: 0.6411 (m-80) cc_final: 0.6127 (m-80)
  outliers start: 12
  outliers final: 3
  residues processed: 129
  average time/residue: 0.1929
  time to fit residues: 32.7490
Evaluate side-chains
  106 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  441 LYS
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 58 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 14 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0270
   chunk 4 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.6440

-------------------------------------------------------------------------------
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 378 HIS
A 598 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.141045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.113218 restraints weight = 16356.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.116411 restraints weight = 9140.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.118669 restraints weight = 6272.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.5163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.846   6717  Z= 0.370
  Angle     :  0.620   6.678   9142  Z= 0.323
  Chirality :  0.044   0.205    964
  Planarity :  0.005   0.046   1172
  Dihedral  :  5.346  36.301    984
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.68 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.98 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.29), residues: 787
  helix:  0.78 (0.25), residues: 400
  sheet:  0.58 (0.82), residues: 42
  loop : -1.10 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.035   0.002   PHE B 375 
 TYR   0.015   0.002   TYR A 237 
 ARG   0.004   0.001   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00235 (    6)
  link_NAG-ASN         : angle       2.10450 (   18)
  hydrogen bonds       : bond        0.04593 (  315)
  hydrogen bonds       : angle       4.71499 (  903)
  metal coordination   : bond        0.59793 (    2)
  SS BOND              : bond        0.00314 (    7)
  SS BOND              : angle       1.29030 (   14)
  covalent geometry    : bond        0.00303 ( 6702)
  covalent geometry    : angle       0.61234 ( 9110)

*********************** 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
  130 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 TRP cc_start: 0.8283 (t-100) cc_final: 0.7635 (t60)
REVERT: A  249 MET cc_start: 0.8353 (mtp) cc_final: 0.7533 (mpp)
REVERT: A  323 MET cc_start: 0.8353 (mmt) cc_final: 0.7246 (mmm)
REVERT: A  366 MET cc_start: 0.8566 (ppp) cc_final: 0.7901 (ppp)
REVERT: A  376 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7896 (tpt)
REVERT: A  441 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8436 (ttpp)
REVERT: A  468 ILE cc_start: 0.8518 (mm) cc_final: 0.8246 (mm)
REVERT: B  347 PHE cc_start: 0.6113 (m-80) cc_final: 0.5722 (m-80)
REVERT: B  349 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8302 (p)
REVERT: B  406 GLU cc_start: 0.7803 (mp0) cc_final: 0.7545 (mp0)
  outliers start: 15
  outliers final: 7
  residues processed: 123
  average time/residue: 0.1849
  time to fit residues: 30.4967
Evaluate side-chains
  109 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
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  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  407 VAL
Chi-restraints excluded: chain B residue  453 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0770
   chunk 35 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.7142

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 HIS
B 439 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.139475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.111819 restraints weight = 16215.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.114994 restraints weight = 9203.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.117194 restraints weight = 6301.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.5605

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= 0.375
  Angle     :  0.622   7.977   9142  Z= 0.327
  Chirality :  0.044   0.198    964
  Planarity :  0.005   0.049   1172
  Dihedral  :  5.158  36.888    984
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.81 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.42 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.29), residues: 787
  helix:  0.80 (0.25), residues: 407
  sheet:  0.37 (0.80), residues: 42
  loop : -1.09 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 594 
 HIS   0.006   0.001   HIS A 345 
 PHE   0.016   0.001   PHE B 490 
 TYR   0.022   0.002   TYR A 243 
 ARG   0.003   0.001   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00200 (    6)
  link_NAG-ASN         : angle       1.99327 (   18)
  hydrogen bonds       : bond        0.04536 (  315)
  hydrogen bonds       : angle       4.68162 (  903)
  metal coordination   : bond        0.60217 (    2)
  SS BOND              : bond        0.00388 (    7)
  SS BOND              : angle       1.58672 (   14)
  covalent geometry    : bond        0.00318 ( 6702)
  covalent geometry    : angle       0.61353 ( 9110)

*********************** 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
  130 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7028 (mmt) cc_final: 0.6480 (mmm)
REVERT: A  163 TRP cc_start: 0.8409 (t-100) cc_final: 0.8144 (t60)
REVERT: A  323 MET cc_start: 0.8287 (mmt) cc_final: 0.7142 (mmm)
REVERT: A  366 MET cc_start: 0.8559 (ppp) cc_final: 0.7919 (ppp)
REVERT: A  376 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7813 (tpt)
REVERT: A  406 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8529 (mm-30)
REVERT: A  441 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8475 (ttpp)
REVERT: B  347 PHE cc_start: 0.6376 (m-80) cc_final: 0.6041 (m-80)
REVERT: B  349 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8324 (p)
REVERT: B  406 GLU cc_start: 0.7863 (mp0) cc_final: 0.7579 (mp0)
  outliers start: 19
  outliers final: 11
  residues processed: 124
  average time/residue: 0.1714
  time to fit residues: 28.6329
Evaluate side-chains
  114 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
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  271 TRP
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  453 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    0.0770
   chunk 64 optimal weight:    0.0470
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.5036

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 HIS
B 439 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.140145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.112750 restraints weight = 16034.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.115875 restraints weight = 9122.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.118012 restraints weight = 6268.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.6056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.852   6717  Z= 0.369
  Angle     :  0.611   6.640   9142  Z= 0.322
  Chirality :  0.044   0.199    964
  Planarity :  0.005   0.055   1172
  Dihedral  :  4.894  35.621    984
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.43 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 21.58 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.29), residues: 787
  helix:  0.85 (0.25), residues: 402
  sheet:  1.04 (0.77), residues: 40
  loop : -1.09 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 473 
 HIS   0.007   0.001   HIS A 374 
 PHE   0.032   0.001   PHE B 375 
 TYR   0.024   0.002   TYR A 243 
 ARG   0.004   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00217 (    6)
  link_NAG-ASN         : angle       1.80007 (   18)
  hydrogen bonds       : bond        0.04445 (  315)
  hydrogen bonds       : angle       4.59025 (  903)
  metal coordination   : bond        0.60240 (    2)
  SS BOND              : bond        0.00526 (    7)
  SS BOND              : angle       2.11888 (   14)
  covalent geometry    : bond        0.00279 ( 6702)
  covalent geometry    : angle       0.60133 ( 9110)

*********************** 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
  128 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.8972 (m110) cc_final: 0.8573 (m-40)
REVERT: A  152 MET cc_start: 0.7101 (mmt) cc_final: 0.6715 (mmm)
REVERT: A  163 TRP cc_start: 0.8481 (t-100) cc_final: 0.8242 (t60)
REVERT: A  249 MET cc_start: 0.8169 (mtp) cc_final: 0.7171 (mpp)
REVERT: A  323 MET cc_start: 0.8262 (mmt) cc_final: 0.7545 (mmm)
REVERT: A  366 MET cc_start: 0.8505 (ppp) cc_final: 0.7887 (ppp)
REVERT: A  376 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8095 (tpp)
REVERT: A  406 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8547 (mm-30)
REVERT: A  441 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8485 (ttpp)
REVERT: A  461 TRP cc_start: 0.9000 (m-10) cc_final: 0.8749 (m-10)
REVERT: B  347 PHE cc_start: 0.6007 (m-80) cc_final: 0.5656 (m-80)
REVERT: B  349 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.8195 (p)
  outliers start: 19
  outliers final: 11
  residues processed: 121
  average time/residue: 0.1664
  time to fit residues: 27.7076
Evaluate side-chains
  110 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
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  261 CYS
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  376 MET
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  362 VAL
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  439 ASN
Chi-restraints excluded: chain B residue  453 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 75 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0060
   chunk 71 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.4334

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 439 ASN
B 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.140028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.112931 restraints weight = 16195.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.116128 restraints weight = 9143.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.118307 restraints weight = 6218.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.6301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6717  Z= 0.122
  Angle     :  0.596   9.406   9142  Z= 0.313
  Chirality :  0.043   0.196    964
  Planarity :  0.005   0.060   1172
  Dihedral  :  4.728  34.010    984
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.30 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.44 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.29), residues: 787
  helix:  0.88 (0.26), residues: 402
  sheet:  0.99 (0.76), residues: 41
  loop : -1.14 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A 473 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.018   0.001   PHE A 464 
 TYR   0.025   0.001   TYR A 243 
 ARG   0.004   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00218 (    6)
  link_NAG-ASN         : angle       1.66334 (   18)
  hydrogen bonds       : bond        0.04315 (  315)
  hydrogen bonds       : angle       4.54538 (  903)
  metal coordination   : bond        0.01258 (    2)
  SS BOND              : bond        0.00426 (    7)
  SS BOND              : angle       1.18706 (   14)
  covalent geometry    : bond        0.00267 ( 6702)
  covalent geometry    : angle       0.59057 ( 9110)

*********************** 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
  125 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.8973 (m110) cc_final: 0.8562 (m-40)
REVERT: A  152 MET cc_start: 0.6893 (mmt) cc_final: 0.6542 (mmm)
REVERT: A  163 TRP cc_start: 0.8464 (t-100) cc_final: 0.8242 (t60)
REVERT: A  306 ARG cc_start: 0.8440 (ttp-170) cc_final: 0.8195 (ttp-170)
REVERT: A  323 MET cc_start: 0.8485 (mmt) cc_final: 0.7379 (mmm)
REVERT: A  366 MET cc_start: 0.8413 (ppp) cc_final: 0.7807 (ppp)
REVERT: A  376 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7852 (tpt)
REVERT: A  406 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8571 (mm-30)
REVERT: A  441 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8517 (ttpp)
REVERT: A  461 TRP cc_start: 0.8899 (m-10) cc_final: 0.8640 (m-10)
REVERT: A  512 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8377 (t80)
REVERT: A  560 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8726 (mt)
REVERT: B  349 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8138 (p)
  outliers start: 25
  outliers final: 13
  residues processed: 118
  average time/residue: 0.1526
  time to fit residues: 25.2241
Evaluate side-chains
  116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
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  261 CYS
Chi-restraints excluded: chain A residue  271 TRP
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  512 PHE
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  439 ASN
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 439 ASN
B 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.137161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.109680 restraints weight = 16152.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.112821 restraints weight = 9102.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.114954 restraints weight = 6236.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.6611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6717  Z= 0.147
  Angle     :  0.612   6.692   9142  Z= 0.322
  Chirality :  0.044   0.187    964
  Planarity :  0.005   0.061   1172
  Dihedral  :  4.883  34.477    984
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.07 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 22.73 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.29), residues: 787
  helix:  0.95 (0.26), residues: 402
  sheet:  0.85 (0.78), residues: 41
  loop : -1.12 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 473 
 HIS   0.006   0.001   HIS A 345 
 PHE   0.030   0.002   PHE B 375 
 TYR   0.024   0.002   TYR A 243 
 ARG   0.005   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00177 (    6)
  link_NAG-ASN         : angle       1.72708 (   18)
  hydrogen bonds       : bond        0.04536 (  315)
  hydrogen bonds       : angle       4.56716 (  903)
  metal coordination   : bond        0.00023 (    2)
  SS BOND              : bond        0.00494 (    7)
  SS BOND              : angle       1.33304 (   14)
  covalent geometry    : bond        0.00333 ( 6702)
  covalent geometry    : angle       0.60550 ( 9110)

*********************** 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
  128 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.9006 (m110) cc_final: 0.8578 (m-40)
REVERT: A  152 MET cc_start: 0.7163 (mmt) cc_final: 0.6795 (mmm)
REVERT: A  163 TRP cc_start: 0.8474 (t-100) cc_final: 0.8267 (t60)
REVERT: A  234 LYS cc_start: 0.9383 (ptmm) cc_final: 0.9134 (pttp)
REVERT: A  280 SER cc_start: 0.8850 (m) cc_final: 0.8621 (p)
REVERT: A  306 ARG cc_start: 0.8508 (ttp-170) cc_final: 0.8267 (ttp-170)
REVERT: A  323 MET cc_start: 0.8498 (mmt) cc_final: 0.7386 (mmm)
REVERT: A  366 MET cc_start: 0.8386 (ppp) cc_final: 0.7794 (ppp)
REVERT: A  376 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7878 (tpt)
REVERT: A  406 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8608 (mm-30)
REVERT: A  441 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8541 (ttpp)
REVERT: A  461 TRP cc_start: 0.8920 (m-10) cc_final: 0.8662 (m-10)
REVERT: A  512 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8351 (t80)
REVERT: A  560 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8788 (mt)
  outliers start: 24
  outliers final: 18
  residues processed: 118
  average time/residue: 0.1730
  time to fit residues: 28.9865
Evaluate side-chains
  121 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
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  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  512 PHE
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  439 ASN
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0020
   chunk 43 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.6788

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 439 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.137315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.109730 restraints weight = 16116.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.112978 restraints weight = 8985.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.115135 restraints weight = 6082.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.6837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6717  Z= 0.136
  Angle     :  0.613   8.096   9142  Z= 0.320
  Chirality :  0.044   0.188    964
  Planarity :  0.005   0.059   1172
  Dihedral  :  4.887  34.703    984
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.56 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.88 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.30), residues: 787
  helix:  1.04 (0.26), residues: 399
  sheet:  0.96 (0.76), residues: 41
  loop : -1.10 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 473 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.014   0.001   PHE A 369 
 TYR   0.027   0.002   TYR A 243 
 ARG   0.007   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00161 (    6)
  link_NAG-ASN         : angle       1.61678 (   18)
  hydrogen bonds       : bond        0.04426 (  315)
  hydrogen bonds       : angle       4.51962 (  903)
  metal coordination   : bond        0.00048 (    2)
  SS BOND              : bond        0.00669 (    7)
  SS BOND              : angle       1.28190 (   14)
  covalent geometry    : bond        0.00304 ( 6702)
  covalent geometry    : angle       0.60768 ( 9110)

*********************** 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
  125 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7913 (ppp) cc_final: 0.7424 (ppp)
REVERT: A  121 ASN cc_start: 0.9028 (m110) cc_final: 0.8697 (m-40)
REVERT: A  152 MET cc_start: 0.7308 (mmt) cc_final: 0.6909 (mmm)
REVERT: A  234 LYS cc_start: 0.9410 (ptmm) cc_final: 0.9153 (pttp)
REVERT: A  280 SER cc_start: 0.8824 (m) cc_final: 0.8597 (p)
REVERT: A  306 ARG cc_start: 0.8515 (ttp-170) cc_final: 0.8160 (ttp-170)
REVERT: A  323 MET cc_start: 0.8486 (mmt) cc_final: 0.7366 (mmm)
REVERT: A  366 MET cc_start: 0.8361 (ppp) cc_final: 0.7762 (ppp)
REVERT: A  376 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7897 (tpt)
REVERT: A  406 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8632 (mm-30)
REVERT: A  441 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8665 (ttpp)
REVERT: A  461 TRP cc_start: 0.8902 (m-10) cc_final: 0.8650 (m-10)
REVERT: A  512 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8325 (t80)
REVERT: A  560 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8806 (mt)
  outliers start: 23
  outliers final: 17
  residues processed: 116
  average time/residue: 0.1634
  time to fit residues: 26.4007
Evaluate side-chains
  116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
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  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  512 PHE
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  439 ASN
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 26 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 439 ASN
B 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.132331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.104324 restraints weight = 16183.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.107349 restraints weight = 9082.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.109443 restraints weight = 6205.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.7230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6717  Z= 0.202
  Angle     :  0.689   9.701   9142  Z= 0.364
  Chirality :  0.046   0.197    964
  Planarity :  0.005   0.058   1172
  Dihedral  :  5.531  38.579    984
  Min Nonbonded Distance : 1.767

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.19 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 23.60 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.29), residues: 787
  helix:  0.98 (0.26), residues: 392
  sheet:  0.29 (0.75), residues: 43
  loop : -1.03 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 473 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.023   0.002   PHE A 592 
 TYR   0.024   0.002   TYR A 243 
 ARG   0.008   0.001   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00336 (    6)
  link_NAG-ASN         : angle       2.02171 (   18)
  hydrogen bonds       : bond        0.05204 (  315)
  hydrogen bonds       : angle       4.78218 (  903)
  metal coordination   : bond        0.00139 (    2)
  SS BOND              : bond        0.00379 (    7)
  SS BOND              : angle       1.54448 (   14)
  covalent geometry    : bond        0.00461 ( 6702)
  covalent geometry    : angle       0.68170 ( 9110)

********************** 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
  125 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.700 
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   82 MET cc_start: 0.8007 (ppp) cc_final: 0.7659 (ppp)
REVERT: A  121 ASN cc_start: 0.9067 (m110) cc_final: 0.8723 (m-40)
REVERT: A  152 MET cc_start: 0.7454 (mmt) cc_final: 0.7106 (mmm)
REVERT: A  234 LYS cc_start: 0.9431 (ptmm) cc_final: 0.9175 (pttp)
REVERT: A  249 MET cc_start: 0.8160 (mtp) cc_final: 0.7086 (mpp)
REVERT: A  280 SER cc_start: 0.8864 (m) cc_final: 0.8657 (p)
REVERT: A  306 ARG cc_start: 0.8527 (ttp-170) cc_final: 0.8226 (ttp-170)
REVERT: A  366 MET cc_start: 0.8594 (ppp) cc_final: 0.7886 (ppp)
REVERT: A  406 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8662 (mm-30)
REVERT: A  441 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8638 (ttpp)
REVERT: A  512 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8431 (t80)
REVERT: A  560 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8888 (mt)
  outliers start: 22
  outliers final: 16
  residues processed: 119
  average time/residue: 0.1549
  time to fit residues: 25.7574
Evaluate side-chains
  115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
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  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  512 PHE
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  439 ASN
Chi-restraints excluded: chain B residue  453 TYR
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 73 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0060
   chunk 67 optimal weight:    0.0070
   chunk 8 optimal weight:    0.0970
   chunk 37 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.4012

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 439 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.137173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.109676 restraints weight = 16257.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.112835 restraints weight = 9089.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.114980 restraints weight = 6161.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.7328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6717  Z= 0.128
  Angle     :  0.653  10.472   9142  Z= 0.335
  Chirality :  0.044   0.187    964
  Planarity :  0.005   0.057   1172
  Dihedral  :  5.010  36.782    984
  Min Nonbonded Distance : 1.771

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.30 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 25.61 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.30), residues: 787
  helix:  1.02 (0.26), residues: 398
  sheet:  0.80 (0.78), residues: 39
  loop : -1.07 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 473 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.024   0.001   PHE A 428 
 TYR   0.036   0.001   TYR A 243 
 ARG   0.007   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00218 (    6)
  link_NAG-ASN         : angle       1.55563 (   18)
  hydrogen bonds       : bond        0.04417 (  315)
  hydrogen bonds       : angle       4.52090 (  903)
  metal coordination   : bond        0.00114 (    2)
  SS BOND              : bond        0.00423 (    7)
  SS BOND              : angle       1.14582 (   14)
  covalent geometry    : bond        0.00276 ( 6702)
  covalent geometry    : angle       0.64941 ( 9110)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2623.84 seconds
wall clock time: 46 minutes 33.52 seconds (2793.52 seconds total)