Starting phenix.real_space_refine
on Thu Jun  5 21:21:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sy2_25514/06_2025/7sy2_25514.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sy2_25514/06_2025/7sy2_25514.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sy2_25514/06_2025/7sy2_25514.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sy2_25514/06_2025/7sy2_25514.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sy2_25514/06_2025/7sy2_25514.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sy2_25514/06_2025/7sy2_25514.cif"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.032
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    4191      2.51       5
     N    1077      2.21       5
     O    1249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6554
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1594
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 4.39, per 1000 atoms: 0.67
  Number of scatterers: 6554
  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    1249      8.00
     N    1077      7.00
     C    4191      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: 1.35
  Conformation dependent library (CDL) restraints added in 839.2 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 7 sheets defined
      57.2% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  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
      removed outlier: 3.502A  pdb=" N   LYS B 386 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.745A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 3.792A  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: 3.751A  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: 3.994A  pdb=" N   VAL E 107 " --> pdb=" O   GLY E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 129
    Processing helix  chain 'E' and resid 146 through 155
      removed outlier: 3.967A  pdb=" N   ILE E 151 " --> pdb=" O   GLY E 147 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.710A  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: 3.659A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.754A  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: 3.801A  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
      removed outlier: 3.583A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.685A  pdb=" N   TYR E 385 " --> pdb=" O   TYR E 381 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 388
      No H-bonds generated for 'chain 'E' and resid 386 through 388'
    Processing helix  chain 'E' and resid 389 through 393
    Processing helix  chain 'E' and resid 397 through 413
      removed outlier: 4.279A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.947A  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: 3.519A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.358A  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: 3.734A  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: 4.434A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.902A  pdb=" N   MET E 557 " --> pdb=" O   LYS E 553 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 565 through 574
    Processing helix  chain 'E' and resid 581 through 588
    Processing helix  chain 'E' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.981A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.835A  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: 3.690A  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: 6.005A  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: 6.335A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    915 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.63

  Time building geometry restraints manager: 1.63 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: 2083
        1.35 -     1.47: 1794
        1.47 -     1.60: 2802
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6737
  Sorted by residual:
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.455 -0.049 2.00e-02 2.50e+03 6.07e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.451 -0.045 2.00e-02 2.50e+03 4.98e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.450 -0.044 2.00e-02 2.50e+03 4.84e+00
  bond pdb=" C1  NAG E 706 "
       pdb=" O5  NAG E 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.27e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.11e+00
  ... (remaining 6732 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 8815
        2.03 -     4.05: 295
        4.05 -     6.08: 35
        6.08 -     8.10: 7
        8.10 -    10.13: 4
  Bond angle restraints: 9156
  Sorted by residual:
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.82  128.95   -6.13 1.42e+00 4.96e-01 1.86e+01
  angle pdb=" CA  CYS E 141 "
        pdb=" CB  CYS E 141 "
        pdb=" SG  CYS E 141 "
      ideal   model   delta    sigma   weight residual
     114.40  123.57   -9.17 2.30e+00 1.89e-01 1.59e+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  115.98   -3.38 1.00e+00 1.00e+00 1.14e+01
  angle pdb=" CB  MET E 323 "
        pdb=" CG  MET E 323 "
        pdb=" SD  MET E 323 "
      ideal   model   delta    sigma   weight residual
     112.70  122.83  -10.13 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" N   TYR B 495 "
        pdb=" CA  TYR B 495 "
        pdb=" C   TYR B 495 "
      ideal   model   delta    sigma   weight residual
     110.52  105.59    4.93 1.48e+00 4.57e-01 1.11e+01
  ... (remaining 9151 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 3687
       17.13 -    34.25: 306
       34.25 -    51.38: 48
       51.38 -    68.51: 13
       68.51 -    85.63: 12
  Dihedral angle restraints: 4066
    sinusoidal: 1727
      harmonic: 2339
  Sorted by residual:
  dihedral pdb=" CB  CYS E 133 "
           pdb=" SG  CYS E 133 "
           pdb=" SG  CYS E 141 "
           pdb=" CB  CYS E 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -43.43  -42.57     1      1.00e+01 1.00e-02 2.53e+01
  dihedral pdb=" SG  CYS B 391 "
           pdb=" CB  CYS B 525 "
           pdb=" SG  CYS B 525 "
           pdb=" CA  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   16.60   62.40     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 -130.73    8.13     0      2.50e+00 1.60e-01 1.06e+01
  ... (remaining 4063 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 713
       0.053 -    0.107: 200
       0.107 -    0.160: 55
       0.160 -    0.213: 8
       0.213 -    0.267: 2
  Chirality restraints: 978
  Sorted by residual:
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" CB  VAL E 581 "
            pdb=" CA  VAL E 581 "
            pdb=" CG1 VAL E 581 "
            pdb=" CG2 VAL E 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.20e+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 975 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 169 "    0.017 2.00e-02 2.50e+03   3.38e-02 1.14e+01
        pdb=" C   ARG E 169 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   ARG E 169 "    0.022 2.00e-02 2.50e+03
        pdb=" N   SER E 170 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP E 168 "    0.014 2.00e-02 2.50e+03   2.74e-02 7.52e+00
        pdb=" C   TRP E 168 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   TRP E 168 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ARG E 169 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR E  41 "   -0.013 2.00e-02 2.50e+03   2.62e-02 6.87e+00
        pdb=" C   TYR E  41 "    0.045 2.00e-02 2.50e+03
        pdb=" O   TYR E  41 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLN E  42 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1934
        2.83 -     3.34: 5949
        3.34 -     3.86: 11371
        3.86 -     4.38: 12856
        4.38 -     4.90: 22341
  Nonbonded interactions: 54451
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.349 3.120
  nonbonded pdb=" OE1 GLU B 406 "
            pdb=" OH  TYR B 495 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.356 3.040
  ... (remaining 54446 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.530
  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:2.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   6750  Z= 0.233
  Angle     :  0.877  12.470   9189  Z= 0.467
  Chirality :  0.055   0.267    978
  Planarity :  0.007   0.065   1177
  Dihedral  : 13.461  85.634   2548
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.86 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.26), residues: 793
  helix: -0.05 (0.23), residues: 385
  sheet:  0.55 (0.66), residues: 53
  loop : -0.59 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E 566 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.031   0.002   PHE E 369 
 TYR   0.029   0.002   TYR E 385 
 ARG   0.007   0.001   ARG E 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00875 (    7)
  link_NAG-ASN         : angle       4.67517 (   21)
  hydrogen bonds       : bond        0.13584 (  321)
  hydrogen bonds       : angle       6.21421 (  915)
  SS BOND              : bond        0.00521 (    6)
  SS BOND              : angle       2.66283 (   12)
  covalent geometry    : bond        0.00498 ( 6737)
  covalent geometry    : angle       0.84419 ( 9156)

*********************** 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
  96 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8467 (m-30) cc_final: 0.8200 (m-30)
REVERT: E  290 ASN cc_start: 0.8480 (t0) cc_final: 0.7701 (t0)
REVERT: E  408 MET cc_start: 0.9425 (mmt) cc_final: 0.9219 (mmt)
REVERT: E  474 MET cc_start: 0.8855 (mmt) cc_final: 0.8342 (mmm)
REVERT: E  498 CYS cc_start: 0.7597 (t) cc_final: 0.6794 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 96
  average time/residue: 0.3095
  time to fit residues: 36.1147
Evaluate side-chains
  48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 31 optimal weight:    0.3980
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0980
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
E 154 ASN
** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 552 GLN
E 586 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.064669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.050608 restraints weight = 21061.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 3.43
r_work: 0.2775 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6750  Z= 0.127
  Angle     :  0.557   8.769   9189  Z= 0.283
  Chirality :  0.040   0.143    978
  Planarity :  0.004   0.041   1177
  Dihedral  :  5.555  51.226   1013
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  6.29 %
    Favored  : 93.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.28), residues: 793
  helix:  1.05 (0.25), residues: 408
  sheet:  0.56 (0.66), residues: 52
  loop : -0.16 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.018   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 385 
 ARG   0.005   0.001   ARG E 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00491 (    7)
  link_NAG-ASN         : angle       3.07141 (   21)
  hydrogen bonds       : bond        0.04324 (  321)
  hydrogen bonds       : angle       4.63937 (  915)
  SS BOND              : bond        0.00461 (    6)
  SS BOND              : angle       2.20529 (   12)
  covalent geometry    : bond        0.00276 ( 6737)
  covalent geometry    : angle       0.53237 ( 9156)

*********************** 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
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8940 (m-30) cc_final: 0.8682 (m-30)
REVERT: B  406 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8937 (mt-10)
REVERT: E  498 CYS cc_start: 0.7970 (t) cc_final: 0.7430 (t)
  outliers start: 4
  outliers final: 2
  residues processed: 54
  average time/residue: 0.2119
  time to fit residues: 15.5482
Evaluate side-chains
  49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain E residue  151 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 39 optimal weight:    0.1980
   chunk 73 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0770
   overall best weight:    0.5540

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.064678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.050544 restraints weight = 21265.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 3.46
r_work: 0.2770 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6750  Z= 0.115
  Angle     :  0.515   8.084   9189  Z= 0.258
  Chirality :  0.040   0.140    978
  Planarity :  0.004   0.034   1177
  Dihedral  :  5.076  52.790   1013
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  7.71 %
    Favored  : 91.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.29), residues: 793
  helix:  1.42 (0.25), residues: 410
  sheet:  0.96 (0.74), residues: 41
  loop :  0.05 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 385 
 ARG   0.004   0.000   ARG E 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00440 (    7)
  link_NAG-ASN         : angle       2.59416 (   21)
  hydrogen bonds       : bond        0.03969 (  321)
  hydrogen bonds       : angle       4.44398 (  915)
  SS BOND              : bond        0.00345 (    6)
  SS BOND              : angle       1.33787 (   12)
  covalent geometry    : bond        0.00252 ( 6737)
  covalent geometry    : angle       0.49795 ( 9156)

*********************** 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
  63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8900 (m-30) cc_final: 0.8636 (m-30)
REVERT: B  406 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8904 (mt-10)
REVERT: E   55 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.8047 (p)
REVERT: E  325 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8196 (tp-100)
REVERT: E  498 CYS cc_start: 0.8041 (t) cc_final: 0.7415 (t)
  outliers start: 8
  outliers final: 2
  residues processed: 61
  average time/residue: 0.2023
  time to fit residues: 16.6943
Evaluate side-chains
  51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  151 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 68 optimal weight:    0.1980
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0670
   chunk 19 optimal weight:    0.3980
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.4118

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.065154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.051084 restraints weight = 21308.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 3.45
r_work: 0.2785 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6750  Z= 0.100
  Angle     :  0.472   5.874   9189  Z= 0.239
  Chirality :  0.039   0.149    978
  Planarity :  0.003   0.035   1177
  Dihedral  :  4.685  54.219   1013
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  9.57 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.29), residues: 793
  helix:  1.59 (0.25), residues: 410
  sheet:  0.87 (0.75), residues: 41
  loop :  0.18 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.012   0.001   PHE E 369 
 TYR   0.009   0.001   TYR E 385 
 ARG   0.003   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00377 (    7)
  link_NAG-ASN         : angle       2.27381 (   21)
  hydrogen bonds       : bond        0.03731 (  321)
  hydrogen bonds       : angle       4.34642 (  915)
  SS BOND              : bond        0.00222 (    6)
  SS BOND              : angle       0.83939 (   12)
  covalent geometry    : bond        0.00213 ( 6737)
  covalent geometry    : angle       0.45886 ( 9156)

*********************** 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
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8912 (m-30) cc_final: 0.8658 (m-30)
REVERT: E   55 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.8031 (p)
REVERT: E  249 MET cc_start: 0.8769 (ttp) cc_final: 0.8504 (ttp)
REVERT: E  325 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8430 (tp40)
REVERT: E  498 CYS cc_start: 0.7765 (t) cc_final: 0.7081 (t)
  outliers start: 6
  outliers final: 3
  residues processed: 57
  average time/residue: 0.1981
  time to fit residues: 15.5490
Evaluate side-chains
  49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  151 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0050
   chunk 49 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.7596

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.063653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.049589 restraints weight = 21155.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 3.44
r_work: 0.2741 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6750  Z= 0.131
  Angle     :  0.487   5.416   9189  Z= 0.250
  Chirality :  0.040   0.134    978
  Planarity :  0.003   0.038   1177
  Dihedral  :  4.632  54.935   1013
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 10.43 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.29), residues: 793
  helix:  1.71 (0.25), residues: 407
  sheet:  0.58 (0.74), residues: 42
  loop :  0.34 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 523 
 TYR   0.010   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00312 (    7)
  link_NAG-ASN         : angle       2.11324 (   21)
  hydrogen bonds       : bond        0.03887 (  321)
  hydrogen bonds       : angle       4.33829 (  915)
  SS BOND              : bond        0.00185 (    6)
  SS BOND              : angle       0.76421 (   12)
  covalent geometry    : bond        0.00289 ( 6737)
  covalent geometry    : angle       0.47690 ( 9156)

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8956 (m-30) cc_final: 0.8710 (m-30)
REVERT: E   55 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8062 (p)
REVERT: E  131 LYS cc_start: 0.8979 (ptmm) cc_final: 0.8724 (ttpp)
REVERT: E  325 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8364 (tp40)
REVERT: E  498 CYS cc_start: 0.8030 (t) cc_final: 0.7276 (t)
  outliers start: 8
  outliers final: 5
  residues processed: 53
  average time/residue: 0.1894
  time to fit residues: 14.2189
Evaluate side-chains
  51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  152 MET
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.8582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.062894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.048821 restraints weight = 21175.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 3.40
r_work: 0.2720 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6750  Z= 0.141
  Angle     :  0.492   5.605   9189  Z= 0.253
  Chirality :  0.040   0.134    978
  Planarity :  0.003   0.041   1177
  Dihedral  :  4.613  55.587   1013
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.00 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.29), residues: 793
  helix:  1.79 (0.25), residues: 401
  sheet:  0.52 (0.74), residues: 42
  loop :  0.44 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.010   0.001   TYR E 516 
 ARG   0.003   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00311 (    7)
  link_NAG-ASN         : angle       2.01427 (   21)
  hydrogen bonds       : bond        0.03921 (  321)
  hydrogen bonds       : angle       4.38055 (  915)
  SS BOND              : bond        0.00206 (    6)
  SS BOND              : angle       0.80000 (   12)
  covalent geometry    : bond        0.00314 ( 6737)
  covalent geometry    : angle       0.48298 ( 9156)

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8954 (m-30) cc_final: 0.8697 (m-30)
REVERT: E   55 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.8059 (p)
REVERT: E  325 GLN cc_start: 0.8856 (tp-100) cc_final: 0.8343 (tp40)
REVERT: E  376 MET cc_start: 0.9147 (tpp) cc_final: 0.8903 (tpp)
REVERT: E  498 CYS cc_start: 0.8131 (t) cc_final: 0.7313 (t)
  outliers start: 9
  outliers final: 5
  residues processed: 55
  average time/residue: 0.1955
  time to fit residues: 14.8248
Evaluate side-chains
  48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  152 MET
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0570
   chunk 10 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 78 optimal weight:    0.0040
   chunk 64 optimal weight:    0.9990
   chunk 11 optimal weight:    0.3980
   chunk 73 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.3710

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.064647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.050001 restraints weight = 21230.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 3.52
r_work: 0.2763 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6750  Z= 0.099
  Angle     :  0.473   6.219   9189  Z= 0.242
  Chirality :  0.039   0.126    978
  Planarity :  0.003   0.042   1177
  Dihedral  :  4.436  56.195   1013
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.57 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.29), residues: 793
  helix:  1.76 (0.25), residues: 408
  sheet:  0.44 (0.75), residues: 42
  loop :  0.50 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.011   0.001   PHE E 523 
 TYR   0.008   0.001   TYR E 385 
 ARG   0.003   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00287 (    7)
  link_NAG-ASN         : angle       1.94274 (   21)
  hydrogen bonds       : bond        0.03652 (  321)
  hydrogen bonds       : angle       4.32747 (  915)
  SS BOND              : bond        0.00332 (    6)
  SS BOND              : angle       0.72427 (   12)
  covalent geometry    : bond        0.00216 ( 6737)
  covalent geometry    : angle       0.46339 ( 9156)

*********************** 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
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8939 (m-30) cc_final: 0.8661 (m-30)
REVERT: E   55 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8040 (p)
REVERT: E  325 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8329 (tp40)
REVERT: E  360 MET cc_start: 0.8763 (ttm) cc_final: 0.8555 (ttm)
  outliers start: 9
  outliers final: 7
  residues processed: 49
  average time/residue: 0.1971
  time to fit residues: 13.5681
Evaluate side-chains
  49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  152 MET
Chi-restraints excluded: chain E residue  332 MET
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0270
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.8440

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.062978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.048902 restraints weight = 21351.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 3.41
r_work: 0.2723 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6750  Z= 0.140
  Angle     :  0.495   6.842   9189  Z= 0.254
  Chirality :  0.040   0.130    978
  Planarity :  0.003   0.043   1177
  Dihedral  :  4.500  56.198   1013
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.57 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.30), residues: 793
  helix:  1.79 (0.25), residues: 408
  sheet:  0.48 (0.77), residues: 42
  loop :  0.59 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 385 
 ARG   0.003   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00290 (    7)
  link_NAG-ASN         : angle       1.91318 (   21)
  hydrogen bonds       : bond        0.03878 (  321)
  hydrogen bonds       : angle       4.33672 (  915)
  SS BOND              : bond        0.00193 (    6)
  SS BOND              : angle       0.73420 (   12)
  covalent geometry    : bond        0.00313 ( 6737)
  covalent geometry    : angle       0.48664 ( 9156)

*********************** 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
  54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8929 (m-30) cc_final: 0.8626 (m-30)
REVERT: E   55 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8021 (p)
REVERT: E  325 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8363 (tp40)
REVERT: E  360 MET cc_start: 0.8831 (ttm) cc_final: 0.8577 (ttm)
REVERT: E  498 CYS cc_start: 0.7968 (t) cc_final: 0.7236 (t)
  outliers start: 8
  outliers final: 7
  residues processed: 51
  average time/residue: 0.1941
  time to fit residues: 14.0383
Evaluate side-chains
  51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  152 MET
Chi-restraints excluded: chain E residue  332 MET
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 41 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   chunk 35 optimal weight:    5.9990
   chunk 72 optimal weight:    0.1980
   chunk 42 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.064376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.049736 restraints weight = 21418.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 3.54
r_work: 0.2751 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6750  Z= 0.108
  Angle     :  0.475   6.349   9189  Z= 0.246
  Chirality :  0.039   0.125    978
  Planarity :  0.003   0.043   1177
  Dihedral  :  4.382  56.360   1013
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.29 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.30), residues: 793
  helix:  1.78 (0.25), residues: 408
  sheet:  0.49 (0.76), residues: 42
  loop :  0.62 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 
 PHE   0.012   0.001   PHE E 523 
 TYR   0.009   0.001   TYR E 385 
 ARG   0.003   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00270 (    7)
  link_NAG-ASN         : angle       1.89744 (   21)
  hydrogen bonds       : bond        0.03664 (  321)
  hydrogen bonds       : angle       4.31963 (  915)
  SS BOND              : bond        0.00196 (    6)
  SS BOND              : angle       0.72984 (   12)
  covalent geometry    : bond        0.00236 ( 6737)
  covalent geometry    : angle       0.46625 ( 9156)

*********************** 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
  53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8973 (m-30) cc_final: 0.8675 (m-30)
REVERT: B  518 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7600 (tt)
REVERT: E   55 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7988 (p)
REVERT: E  325 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8366 (tp40)
REVERT: E  360 MET cc_start: 0.8789 (ttm) cc_final: 0.8547 (ttm)
  outliers start: 9
  outliers final: 7
  residues processed: 50
  average time/residue: 0.1866
  time to fit residues: 13.4587
Evaluate side-chains
  51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  152 MET
Chi-restraints excluded: chain E residue  332 MET
Chi-restraints excluded: chain E residue  463 VAL
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
B 498 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.060593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.046412 restraints weight = 21667.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 3.41
r_work: 0.2666 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6750  Z= 0.230
  Angle     :  0.568   7.784   9189  Z= 0.294
  Chirality :  0.042   0.144    978
  Planarity :  0.004   0.046   1177
  Dihedral  :  4.812  56.059   1013
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.43 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.30), residues: 793
  helix:  1.70 (0.25), residues: 402
  sheet:  0.43 (0.75), residues: 42
  loop :  0.69 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.017   0.001   PHE E 369 
 TYR   0.015   0.001   TYR E 385 
 ARG   0.003   0.001   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00336 (    7)
  link_NAG-ASN         : angle       2.04158 (   21)
  hydrogen bonds       : bond        0.04321 (  321)
  hydrogen bonds       : angle       4.52353 (  915)
  SS BOND              : bond        0.00190 (    6)
  SS BOND              : angle       0.87872 (   12)
  covalent geometry    : bond        0.00516 ( 6737)
  covalent geometry    : angle       0.56006 ( 9156)

********************** 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
  53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  518 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7580 (tt)
REVERT: E   55 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7959 (p)
REVERT: E  325 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8389 (tp40)
REVERT: E  498 CYS cc_start: 0.8348 (t) cc_final: 0.7230 (t)
  outliers start: 9
  outliers final: 7
  residues processed: 50
  average time/residue: 0.1842
  time to fit residues: 13.2817
Evaluate side-chains
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  151 ILE
Chi-restraints excluded: chain E residue  152 MET
Chi-restraints excluded: chain E residue  332 MET
Chi-restraints excluded: chain E residue  463 VAL
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   chunk 67 optimal weight:    0.4980
   chunk 52 optimal weight:    2.9990
   chunk 30 optimal weight:    0.3980
   chunk 19 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.063025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.049013 restraints weight = 21427.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 3.40
r_work: 0.2722 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6750  Z= 0.120
  Angle     :  0.486   5.328   9189  Z= 0.252
  Chirality :  0.040   0.127    978
  Planarity :  0.003   0.046   1177
  Dihedral  :  4.553  56.592   1013
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.00 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.30), residues: 793
  helix:  1.69 (0.25), residues: 407
  sheet:  0.40 (0.76), residues: 42
  loop :  0.65 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 315 
 TYR   0.010   0.001   TYR E 385 
 ARG   0.003   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00285 (    7)
  link_NAG-ASN         : angle       2.03161 (   21)
  hydrogen bonds       : bond        0.03840 (  321)
  hydrogen bonds       : angle       4.44101 (  915)
  SS BOND              : bond        0.00198 (    6)
  SS BOND              : angle       0.80055 (   12)
  covalent geometry    : bond        0.00266 ( 6737)
  covalent geometry    : angle       0.47576 ( 9156)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3264.44 seconds
wall clock time: 57 minutes 0.39 seconds (3420.39 seconds total)