Starting phenix.real_space_refine
on Thu Jul 24 21:34:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dlq_27510/07_2025/8dlq_27510.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dlq_27510/07_2025/8dlq_27510.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dlq_27510/07_2025/8dlq_27510.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dlq_27510/07_2025/8dlq_27510.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dlq_27510/07_2025/8dlq_27510.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dlq_27510/07_2025/8dlq_27510.cif"
  }
  resolution = 2.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4190      2.51       5
     N    1077      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6552
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1592
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 5.75, per 1000 atoms: 0.88
  Number of scatterers: 6552
  At special positions: 0
  Unit cell: (80, 83, 122, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1248      8.00
     N    1077      7.00
     C    4190      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    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
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 530 " - pdb=" SG  CYS E 542 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B1301 " - " ASN B 343 "
      " NAG E 701 " - " ASN E  53 "
      " NAG E 702 " - " ASN E  90 "
      " NAG E 703 " - " ASN E 103 "
      " NAG E 704 " - " ASN E 322 "
      " NAG E 705 " - " ASN E 432 "
      " NAG E 706 " - " ASN E 546 "
  Time building additional restraints: 1.57
  Conformation dependent library (CDL) restraints added in 960.0 milliseconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 7 sheets defined
      57.8% alpha, 6.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.013A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.568A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 3.645A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
    Processing helix  chain 'E' and resid 82 through 83
      No H-bonds generated for 'chain 'E' and resid 82 through 83'
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.692A  pdb=" N   GLU E  87 " --> pdb=" O   PRO E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 101
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 4.030A  pdb=" N   VAL E 107 " --> pdb=" O   GLY E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 129
    Processing helix  chain 'E' and resid 147 through 155
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.693A  pdb=" N   VAL E 185 " --> pdb=" O   GLU E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 205
    Processing helix  chain 'E' and resid 206 through 208
      No H-bonds generated for 'chain 'E' and resid 206 through 208'
    Processing helix  chain 'E' and resid 218 through 252
      removed outlier: 3.742A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLU E 232 " --> pdb=" O   HIS E 228 " (cutoff:3.500A)
      Proline residue:  E 235  - end of helix
    Processing helix  chain 'E' and resid 265 through 267
      No H-bonds generated for 'chain 'E' and resid 265 through 267'
    Processing helix  chain 'E' and resid 275 through 279
      removed outlier: 3.793A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 300
    Processing helix  chain 'E' and resid 303 through 318
    Processing helix  chain 'E' and resid 324 through 331
    Processing helix  chain 'E' and resid 365 through 385
    Processing helix  chain 'E' and resid 386 through 388
      No H-bonds generated for 'chain 'E' and resid 386 through 388'
    Processing helix  chain 'E' and resid 389 through 393
    Processing helix  chain 'E' and resid 397 through 413
      removed outlier: 4.296A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   MET E 408 " --> pdb=" O   VAL E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 421
    Processing helix  chain 'E' and resid 431 through 447
      removed outlier: 3.509A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.315A  pdb=" N   PHE E 452 " --> pdb=" O   GLY E 448 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 469 through 471
      No H-bonds generated for 'chain 'E' and resid 469 through 471'
    Processing helix  chain 'E' and resid 472 through 484
    Processing helix  chain 'E' and resid 499 through 502
      removed outlier: 3.654A  pdb=" N   SER E 502 " --> pdb=" O   ASP E 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 499 through 502'
    Processing helix  chain 'E' and resid 503 through 508
    Processing helix  chain 'E' and resid 512 through 533
      removed outlier: 4.420A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.851A  pdb=" N   MET E 557 " --> pdb=" O   LYS E 553 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 565 through 574
    Processing helix  chain 'E' and resid 581 through 588
    Processing helix  chain 'E' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.864A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132
      removed outlier: 3.578A  pdb=" N   LEU E 142 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263
      removed outlier: 6.123A  pdb=" N   LEU E 262 " --> pdb=" O   VAL E 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352
      removed outlier: 6.521A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    326 hydrogen bonds defined for protein.
    924 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: 1.87

  Time building geometry restraints manager: 1.93 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2079
        1.35 -     1.47: 1810
        1.47 -     1.60: 2788
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6735
  Sorted by residual:
  bond pdb=" C1  NAG E 701 "
       pdb=" O5  NAG E 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.489 -0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.459 -0.053 2.00e-02 2.50e+03 6.95e+00
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.52e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.453 -0.047 2.00e-02 2.50e+03 5.58e+00
  bond pdb=" C   GLU E 145 "
       pdb=" N   PRO E 146 "
    ideal  model  delta    sigma   weight residual
    1.334  1.388 -0.054 2.34e-02 1.83e+03 5.31e+00
  ... (remaining 6730 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 8629
        1.80 -     3.61: 455
        3.61 -     5.41: 49
        5.41 -     7.21: 15
        7.21 -     9.01: 6
  Bond angle restraints: 9154
  Sorted by residual:
  angle pdb=" CA  TYR B 495 "
        pdb=" CB  TYR B 495 "
        pdb=" CG  TYR B 495 "
      ideal   model   delta    sigma   weight residual
     113.90  122.91   -9.01 1.80e+00 3.09e-01 2.51e+01
  angle pdb=" CA  TYR E 385 "
        pdb=" CB  TYR E 385 "
        pdb=" CG  TYR E 385 "
      ideal   model   delta    sigma   weight residual
     113.90  122.12   -8.22 1.80e+00 3.09e-01 2.08e+01
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.36  128.19   -5.83 1.42e+00 4.96e-01 1.69e+01
  angle pdb=" CA  ASN E 437 "
        pdb=" CB  ASN E 437 "
        pdb=" CG  ASN E 437 "
      ideal   model   delta    sigma   weight residual
     112.60  116.03   -3.43 1.00e+00 1.00e+00 1.18e+01
  angle pdb=" CA  ASN B 360 "
        pdb=" CB  ASN B 360 "
        pdb=" CG  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     112.60  115.96   -3.36 1.00e+00 1.00e+00 1.13e+01
  ... (remaining 9149 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 3690
       16.95 -    33.90: 309
       33.90 -    50.85: 38
       50.85 -    67.80: 17
       67.80 -    84.75: 10
  Dihedral angle restraints: 4064
    sinusoidal: 1725
      harmonic: 2339
  Sorted by residual:
  dihedral pdb=" SG  CYS B 391 "
           pdb=" CB  CYS B 525 "
           pdb=" SG  CYS B 525 "
           pdb=" CA  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   15.31   63.69     1      2.00e+01 2.50e-03 1.34e+01
  dihedral pdb=" SG  CYS E 133 "
           pdb=" CB  CYS E 141 "
           pdb=" SG  CYS E 141 "
           pdb=" CA  CYS E 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   16.53   62.47     1      2.00e+01 2.50e-03 1.29e+01
  dihedral pdb=" C   ASN B 360 "
           pdb=" N   ASN B 360 "
           pdb=" CA  ASN B 360 "
           pdb=" CB  ASN B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.95    8.35     0      2.50e+00 1.60e-01 1.12e+01
  ... (remaining 4061 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 687
       0.053 -    0.106: 213
       0.106 -    0.159: 63
       0.159 -    0.212: 14
       0.212 -    0.265: 2
  Chirality restraints: 979
  Sorted by residual:
  chirality pdb=" CB  VAL E 581 "
            pdb=" CA  VAL E 581 "
            pdb=" CG1 VAL E 581 "
            pdb=" CG2 VAL E 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  ASN E 437 "
            pdb=" N   ASN E 437 "
            pdb=" C   ASN E 437 "
            pdb=" CB  ASN E 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 976 not shown)

  Planarity restraints: 1183
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 169 "    0.014 2.00e-02 2.50e+03   2.91e-02 8.48e+00
        pdb=" C   ARG E 169 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ARG E 169 "    0.019 2.00e-02 2.50e+03
        pdb=" N   SER E 170 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 495 "   -0.030 2.00e-02 2.50e+03   1.96e-02 7.68e+00
        pdb=" CG  TYR B 495 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 495 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 495 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 495 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 495 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 495 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 495 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.046 5.00e-02 4.00e+02   6.90e-02 7.62e+00
        pdb=" N   PRO E 590 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1180 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1891
        2.82 -     3.34: 6027
        3.34 -     3.86: 11482
        3.86 -     4.38: 13057
        4.38 -     4.90: 22523
  Nonbonded interactions: 54980
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" OH  TYR E 237 "
            pdb=" O   VAL E 485 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.384 3.040
  ... (remaining 54975 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.490
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     21.030
  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:             0.010
  Load rotamer database and sin/cos tables:26.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083   6748  Z= 0.272
  Angle     :  0.939  11.763   9187  Z= 0.527
  Chirality :  0.059   0.265    979
  Planarity :  0.007   0.069   1176
  Dihedral  : 13.162  84.755   2546
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.29 %
    Favored  : 95.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.27), residues: 793
  helix:  0.75 (0.24), residues: 391
  sheet:  1.02 (0.65), residues: 42
  loop : -0.35 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 566 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.029   0.003   PHE E 369 
 TYR   0.046   0.002   TYR B 495 
 ARG   0.010   0.001   ARG E 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00918 (    7)
  link_NAG-ASN         : angle       4.79484 (   21)
  hydrogen bonds       : bond        0.14365 (  326)
  hydrogen bonds       : angle       6.28092 (  924)
  SS BOND              : bond        0.00637 (    6)
  SS BOND              : angle       2.29191 (   12)
  covalent geometry    : bond        0.00587 ( 6735)
  covalent geometry    : angle       0.90869 ( 9154)

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.796 
Fit side-chains
REVERT: B  386 LYS cc_start: 0.8764 (pttm) cc_final: 0.8134 (pttm)
REVERT: B  390 LEU cc_start: 0.8852 (mt) cc_final: 0.8415 (mt)
REVERT: E  117 ASN cc_start: 0.8976 (t0) cc_final: 0.8351 (p0)
REVERT: E  121 ASN cc_start: 0.8679 (m-40) cc_final: 0.8439 (m110)
  outliers start: 3
  outliers final: 0
  residues processed: 93
  average time/residue: 1.7827
  time to fit residues: 173.6421
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 498 GLN
E  42 GLN
E 374 HIS
E 552 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.066441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.049834 restraints weight = 17467.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 3.08
r_work: 0.2658 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6748  Z= 0.162
  Angle     :  0.591   9.102   9187  Z= 0.299
  Chirality :  0.042   0.147    979
  Planarity :  0.005   0.042   1176
  Dihedral  :  5.017  49.335   1013
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.29 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.28), residues: 793
  helix:  1.47 (0.25), residues: 398
  sheet:  1.00 (0.73), residues: 42
  loop : -0.08 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.018   0.001   PHE E 369 
 TYR   0.024   0.001   TYR B 495 
 ARG   0.005   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00494 (    7)
  link_NAG-ASN         : angle       3.28113 (   21)
  hydrogen bonds       : bond        0.04793 (  326)
  hydrogen bonds       : angle       4.89743 (  924)
  SS BOND              : bond        0.00350 (    6)
  SS BOND              : angle       1.31892 (   12)
  covalent geometry    : bond        0.00365 ( 6735)
  covalent geometry    : angle       0.56849 ( 9154)

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: B  518 LEU cc_start: 0.8464 (tm) cc_final: 0.8255 (mt)
REVERT: B  528 LYS cc_start: 0.3733 (OUTLIER) cc_final: 0.3093 (pttp)
REVERT: E  117 ASN cc_start: 0.9123 (t0) cc_final: 0.8431 (p0)
REVERT: E  121 ASN cc_start: 0.8976 (m-40) cc_final: 0.8643 (m110)
  outliers start: 11
  outliers final: 3
  residues processed: 67
  average time/residue: 1.3861
  time to fit residues: 97.6566
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  579 MET
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 39 optimal weight:    0.1980
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0370
   overall best weight:    0.5060

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.067774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.050865 restraints weight = 17375.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 3.08
r_work: 0.2694 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6748  Z= 0.123
  Angle     :  0.553  11.205   9187  Z= 0.278
  Chirality :  0.040   0.125    979
  Planarity :  0.004   0.042   1176
  Dihedral  :  4.816  52.587   1013
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.13 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.14 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.29), residues: 793
  helix:  1.73 (0.26), residues: 398
  sheet:  1.06 (0.77), residues: 42
  loop :  0.15 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.020   0.001   TYR B 495 
 ARG   0.004   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00431 (    7)
  link_NAG-ASN         : angle       2.74817 (   21)
  hydrogen bonds       : bond        0.04241 (  326)
  hydrogen bonds       : angle       4.47817 (  924)
  SS BOND              : bond        0.00268 (    6)
  SS BOND              : angle       1.16505 (   12)
  covalent geometry    : bond        0.00272 ( 6735)
  covalent geometry    : angle       0.53651 ( 9154)

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
REVERT: B  528 LYS cc_start: 0.3592 (OUTLIER) cc_final: 0.3255 (pttp)
REVERT: E  117 ASN cc_start: 0.9140 (t0) cc_final: 0.8433 (p0)
REVERT: E  121 ASN cc_start: 0.8983 (m-40) cc_final: 0.8627 (m110)
REVERT: E  291 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8058 (pp)
REVERT: E  480 MET cc_start: 0.9080 (mtp) cc_final: 0.8838 (mtm)
REVERT: E  483 GLU cc_start: 0.8986 (tp30) cc_final: 0.8540 (tm-30)
  outliers start: 10
  outliers final: 2
  residues processed: 63
  average time/residue: 1.5893
  time to fit residues: 105.0160
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.066395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.049357 restraints weight = 17828.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 3.11
r_work: 0.2660 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6748  Z= 0.144
  Angle     :  0.539  10.504   9187  Z= 0.267
  Chirality :  0.040   0.125    979
  Planarity :  0.004   0.043   1176
  Dihedral  :  4.739  53.420   1013
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.14 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.29), residues: 793
  helix:  1.83 (0.26), residues: 400
  sheet:  0.92 (0.79), residues: 42
  loop :  0.20 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.021   0.001   TYR B 495 
 ARG   0.004   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00351 (    7)
  link_NAG-ASN         : angle       2.47784 (   21)
  hydrogen bonds       : bond        0.04356 (  326)
  hydrogen bonds       : angle       4.37725 (  924)
  SS BOND              : bond        0.00258 (    6)
  SS BOND              : angle       1.08591 (   12)
  covalent geometry    : bond        0.00323 ( 6735)
  covalent geometry    : angle       0.52538 ( 9154)

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.9126 (t80) cc_final: 0.8912 (t80)
REVERT: B  528 LYS cc_start: 0.3792 (OUTLIER) cc_final: 0.3240 (pttp)
REVERT: E  291 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8059 (pp)
REVERT: E  483 GLU cc_start: 0.8986 (tp30) cc_final: 0.8548 (tm-30)
  outliers start: 16
  outliers final: 5
  residues processed: 68
  average time/residue: 1.4309
  time to fit residues: 102.2441
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.0782

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.064813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.047840 restraints weight = 17650.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.2764 rms_B_bonded: 3.06
r_work: 0.2618 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6748  Z= 0.185
  Angle     :  0.553   7.426   9187  Z= 0.278
  Chirality :  0.041   0.127    979
  Planarity :  0.004   0.042   1176
  Dihedral  :  4.788  54.499   1013
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 13.57 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.29), residues: 793
  helix:  1.76 (0.26), residues: 398
  sheet:  0.93 (0.80), residues: 42
  loop :  0.33 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.018   0.001   PHE E 369 
 TYR   0.020   0.001   TYR B 495 
 ARG   0.005   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00312 (    7)
  link_NAG-ASN         : angle       2.41805 (   21)
  hydrogen bonds       : bond        0.04593 (  326)
  hydrogen bonds       : angle       4.44718 (  924)
  SS BOND              : bond        0.00300 (    6)
  SS BOND              : angle       1.14783 (   12)
  covalent geometry    : bond        0.00426 ( 6735)
  covalent geometry    : angle       0.54065 ( 9154)

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.9172 (t80) cc_final: 0.8966 (t80)
REVERT: B  528 LYS cc_start: 0.3857 (OUTLIER) cc_final: 0.3422 (pttp)
REVERT: E  483 GLU cc_start: 0.8966 (tp30) cc_final: 0.8531 (tm-30)
REVERT: E  534 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9061 (mtpp)
  outliers start: 14
  outliers final: 5
  residues processed: 60
  average time/residue: 1.6028
  time to fit residues: 100.7260
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  534 LYS
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0370
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.7262

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

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.065405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.048842 restraints weight = 17504.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.2787 rms_B_bonded: 3.01
r_work: 0.2644 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6748  Z= 0.143
  Angle     :  0.528   6.722   9187  Z= 0.265
  Chirality :  0.040   0.127    979
  Planarity :  0.003   0.041   1176
  Dihedral  :  4.694  55.474   1013
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.14 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.30), residues: 793
  helix:  1.71 (0.26), residues: 406
  sheet:  0.91 (0.80), residues: 42
  loop :  0.32 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.018   0.001   TYR B 495 
 ARG   0.006   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00306 (    7)
  link_NAG-ASN         : angle       2.30248 (   21)
  hydrogen bonds       : bond        0.04300 (  326)
  hydrogen bonds       : angle       4.37780 (  924)
  SS BOND              : bond        0.00302 (    6)
  SS BOND              : angle       1.11388 (   12)
  covalent geometry    : bond        0.00325 ( 6735)
  covalent geometry    : angle       0.51556 ( 9154)

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.9174 (t80) cc_final: 0.8939 (t80)
REVERT: B  518 LEU cc_start: 0.8874 (mt) cc_final: 0.8454 (tt)
REVERT: B  528 LYS cc_start: 0.3852 (OUTLIER) cc_final: 0.3395 (pttp)
REVERT: E  483 GLU cc_start: 0.8947 (tp30) cc_final: 0.8537 (tm-30)
REVERT: E  534 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9204 (mmmm)
  outliers start: 10
  outliers final: 4
  residues processed: 59
  average time/residue: 1.6161
  time to fit residues: 100.0318
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  534 LYS
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0770
   chunk 42 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 60 optimal weight:    0.1980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.5738

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.066129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.049484 restraints weight = 17634.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 3.03
r_work: 0.2657 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6748  Z= 0.126
  Angle     :  0.520   7.109   9187  Z= 0.261
  Chirality :  0.040   0.126    979
  Planarity :  0.003   0.040   1176
  Dihedral  :  4.625  55.802   1013
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.43 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.30), residues: 793
  helix:  1.78 (0.26), residues: 406
  sheet:  0.92 (0.79), residues: 42
  loop :  0.36 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.017   0.001   TYR B 495 
 ARG   0.006   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00305 (    7)
  link_NAG-ASN         : angle       2.19666 (   21)
  hydrogen bonds       : bond        0.04133 (  326)
  hydrogen bonds       : angle       4.33312 (  924)
  SS BOND              : bond        0.00293 (    6)
  SS BOND              : angle       1.10624 (   12)
  covalent geometry    : bond        0.00285 ( 6735)
  covalent geometry    : angle       0.50820 ( 9154)

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.9186 (t80) cc_final: 0.8967 (t80)
REVERT: B  518 LEU cc_start: 0.8918 (mt) cc_final: 0.8494 (tt)
REVERT: B  528 LYS cc_start: 0.3899 (OUTLIER) cc_final: 0.3526 (pttp)
REVERT: E  291 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7732 (mm)
REVERT: E  483 GLU cc_start: 0.8971 (tp30) cc_final: 0.8544 (tm-30)
REVERT: E  534 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.9172 (mmmm)
REVERT: E  613 TYR cc_start: 0.6400 (t80) cc_final: 0.6144 (t80)
  outliers start: 15
  outliers final: 5
  residues processed: 65
  average time/residue: 1.3415
  time to fit residues: 91.8663
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  534 LYS
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 45 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 31 optimal weight:    7.9990
   chunk 40 optimal weight:    0.3980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.9384

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.065170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.048396 restraints weight = 17758.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 3.05
r_work: 0.2629 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6748  Z= 0.168
  Angle     :  0.553   7.885   9187  Z= 0.276
  Chirality :  0.041   0.128    979
  Planarity :  0.004   0.040   1176
  Dihedral  :  4.683  56.150   1013
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 15.43 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.30), residues: 793
  helix:  1.77 (0.26), residues: 406
  sheet:  0.87 (0.79), residues: 42
  loop :  0.39 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.017   0.001   PHE E 369 
 TYR   0.019   0.001   TYR B 495 
 ARG   0.008   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00270 (    7)
  link_NAG-ASN         : angle       2.20607 (   21)
  hydrogen bonds       : bond        0.04345 (  326)
  hydrogen bonds       : angle       4.36193 (  924)
  SS BOND              : bond        0.00330 (    6)
  SS BOND              : angle       1.11088 (   12)
  covalent geometry    : bond        0.00389 ( 6735)
  covalent geometry    : angle       0.54228 ( 9154)

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.9201 (t80) cc_final: 0.8966 (t80)
REVERT: B  390 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8919 (mp)
REVERT: B  518 LEU cc_start: 0.8928 (mt) cc_final: 0.8489 (tt)
REVERT: B  528 LYS cc_start: 0.3943 (OUTLIER) cc_final: 0.3566 (pttp)
REVERT: E  483 GLU cc_start: 0.8983 (tp30) cc_final: 0.8588 (tm-30)
REVERT: E  534 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9207 (mmmm)
  outliers start: 11
  outliers final: 4
  residues processed: 59
  average time/residue: 1.3691
  time to fit residues: 85.0636
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  534 LYS
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0270
   chunk 4 optimal weight:    0.2980
   chunk 61 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 20 optimal weight:    0.1980
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    0.2980
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.3038

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.067655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.051105 restraints weight = 17709.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 3.06
r_work: 0.2703 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6748  Z= 0.105
  Angle     :  0.521   8.817   9187  Z= 0.258
  Chirality :  0.039   0.123    979
  Planarity :  0.003   0.040   1176
  Dihedral  :  4.471  56.660   1013
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 16.43 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.30), residues: 793
  helix:  1.83 (0.26), residues: 412
  sheet:  0.92 (0.80), residues: 42
  loop :  0.46 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.028   0.001   TYR E 613 
 ARG   0.008   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00301 (    7)
  link_NAG-ASN         : angle       2.05646 (   21)
  hydrogen bonds       : bond        0.03782 (  326)
  hydrogen bonds       : angle       4.25027 (  924)
  SS BOND              : bond        0.00259 (    6)
  SS BOND              : angle       1.04566 (   12)
  covalent geometry    : bond        0.00235 ( 6735)
  covalent geometry    : angle       0.51150 ( 9154)

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
REVERT: B  390 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8950 (mp)
REVERT: B  462 LYS cc_start: 0.8820 (mmtm) cc_final: 0.8573 (mmmm)
REVERT: B  518 LEU cc_start: 0.8996 (mt) cc_final: 0.8571 (tt)
REVERT: B  528 LYS cc_start: 0.4043 (OUTLIER) cc_final: 0.3582 (pttp)
REVERT: E  483 GLU cc_start: 0.8942 (tp30) cc_final: 0.8522 (tm-30)
  outliers start: 6
  outliers final: 3
  residues processed: 59
  average time/residue: 1.3961
  time to fit residues: 86.7420
Evaluate side-chains
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.066166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.049234 restraints weight = 17660.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 3.06
r_work: 0.2659 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6748  Z= 0.137
  Angle     :  0.538   8.904   9187  Z= 0.269
  Chirality :  0.040   0.125    979
  Planarity :  0.004   0.041   1176
  Dihedral  :  4.511  56.256   1013
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 17.29 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.30), residues: 793
  helix:  1.84 (0.26), residues: 412
  sheet:  1.06 (0.81), residues: 42
  loop :  0.54 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.016   0.001   TYR B 495 
 ARG   0.008   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00272 (    7)
  link_NAG-ASN         : angle       2.03747 (   21)
  hydrogen bonds       : bond        0.04041 (  326)
  hydrogen bonds       : angle       4.25722 (  924)
  SS BOND              : bond        0.00292 (    6)
  SS BOND              : angle       1.05434 (   12)
  covalent geometry    : bond        0.00316 ( 6735)
  covalent geometry    : angle       0.52837 ( 9154)

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
REVERT: B  390 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8978 (mp)
REVERT: B  462 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8579 (mmmm)
REVERT: B  518 LEU cc_start: 0.9009 (mt) cc_final: 0.8578 (tt)
REVERT: B  528 LYS cc_start: 0.4044 (OUTLIER) cc_final: 0.3585 (pttp)
REVERT: E  483 GLU cc_start: 0.8927 (tp30) cc_final: 0.8570 (tm-30)
  outliers start: 4
  outliers final: 2
  residues processed: 55
  average time/residue: 1.5545
  time to fit residues: 90.4392
Evaluate side-chains
  54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  574 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 47 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.065692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.048976 restraints weight = 17912.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 3.06
r_work: 0.2642 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6748  Z= 0.145
  Angle     :  0.551   8.830   9187  Z= 0.275
  Chirality :  0.040   0.126    979
  Planarity :  0.004   0.041   1176
  Dihedral  :  4.562  56.416   1013
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 17.00 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.30), residues: 793
  helix:  1.80 (0.26), residues: 407
  sheet:  1.04 (0.81), residues: 42
  loop :  0.49 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.017   0.001   TYR B 495 
 ARG   0.009   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00273 (    7)
  link_NAG-ASN         : angle       2.08570 (   21)
  hydrogen bonds       : bond        0.04147 (  326)
  hydrogen bonds       : angle       4.28601 (  924)
  SS BOND              : bond        0.00289 (    6)
  SS BOND              : angle       1.07162 (   12)
  covalent geometry    : bond        0.00335 ( 6735)
  covalent geometry    : angle       0.54159 ( 9154)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5218.67 seconds
wall clock time: 91 minutes 3.97 seconds (5463.97 seconds total)