Starting phenix.real_space_refine
on Thu Jun  5 20:41:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sxy_25510/06_2025/7sxy_25510.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sxy_25510/06_2025/7sxy_25510.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sxy_25510/06_2025/7sxy_25510.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sxy_25510/06_2025/7sxy_25510.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sxy_25510/06_2025/7sxy_25510.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sxy_25510/06_2025/7sxy_25510.cif"
  }
  resolution = 2.79
  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=  -0.002 sd=   0.036
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    1080      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: 6557
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1590
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4869
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
      Conformer: "B"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
          bond proxies already assigned to first conformer: 4990
    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: 7.57, per 1000 atoms: 1.15
  Number of scatterers: 6557
  At special positions: 0
  Unit cell: (80, 83, 121, 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    1080      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: 1.34
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1502

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 7 sheets defined
      57.8% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  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 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.674A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 3.832A  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: 3.742A  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: 4.034A  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: 3.942A  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: 3.707A  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: 3.682A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.762A  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: 3.765A  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: 3.545A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.658A  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: 4.219A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.937A  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
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.344A  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: 3.706A  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: 4.397A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.905A  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: 3.860A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.772A  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: 3.657A  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: 6.069A  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: 6.304A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    325 hydrogen bonds defined for protein.
    917 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: 1.65

  Time building geometry restraints manager: 1.55 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: 2087
        1.35 -     1.47: 1785
        1.47 -     1.60: 2811
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6741
  Sorted by residual:
  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 6.50e+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 5.63e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.38e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.07e+00
  bond pdb=" C1  NAG E 706 "
       pdb=" O5  NAG E 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.75e+00
  ... (remaining 6736 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 8820
        2.02 -     4.05: 297
        4.05 -     6.07: 35
        6.07 -     8.09: 7
        8.09 -    10.12: 4
  Bond angle restraints: 9163
  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  128.94   -6.12 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  123.47   -9.07 2.30e+00 1.89e-01 1.55e+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  122.82  -10.12 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" N   LYS E 234 "
        pdb=" CA  LYS E 234 "
        pdb=" C   LYS E 234 "
      ideal   model   delta    sigma   weight residual
     113.16  117.77   -4.61 1.42e+00 4.96e-01 1.05e+01
  ... (remaining 9158 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 3701
       17.13 -    34.25: 306
       34.25 -    51.37: 42
       51.37 -    68.50: 10
       68.50 -    85.62: 12
  Dihedral angle restraints: 4071
    sinusoidal: 1729
      harmonic: 2342
  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  -43.13  -42.87     1      1.00e+01 1.00e-02 2.56e+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   16.37   62.63     1      2.00e+01 2.50e-03 1.30e+01
  dihedral pdb=" CA  ALA E 396 "
           pdb=" C   ALA E 396 "
           pdb=" N   ASN E 397 "
           pdb=" CA  ASN E 397 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.63   16.37     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 4068 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 698
       0.051 -    0.102: 202
       0.102 -    0.153: 63
       0.153 -    0.203: 13
       0.203 -    0.254: 3
  Chirality restraints: 979
  Sorted by residual:
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.62e+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   -2.39   -0.24 2.00e-01 2.50e+01 1.42e+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 1.06e+00
  ... (remaining 976 not shown)

  Planarity restraints: 1186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 169 "    0.017 2.00e-02 2.50e+03   3.40e-02 1.16e+01
        pdb=" C   ARG E 169 "   -0.059 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   2.73e-02 7.43e+00
        pdb=" C   TRP E 168 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   TRP E 168 "    0.017 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=" C   GLU E 589 "   -0.043 5.00e-02 4.00e+02   6.54e-02 6.84e+00
        pdb=" N   PRO E 590 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 1183 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1911
        2.82 -     3.34: 6008
        3.34 -     3.86: 11540
        3.86 -     4.38: 13065
        4.38 -     4.90: 22546
  Nonbonded interactions: 55070
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OG1 THR B 500 "
            pdb=" OH  TYR E  41 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OE1 GLU B 406 "
            pdb=" OH  TYR B 495 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" OH  TYR E 237 "
            pdb=" O   VAL E 485 "
     model   vdw
     2.353 3.040
  ... (remaining 55065 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=0.50 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:             5.410
  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:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.990
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:15.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
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   0.057   6754  Z= 0.242
  Angle     :  0.871  11.463   9196  Z= 0.462
  Chirality :  0.056   0.254    979
  Planarity :  0.007   0.065   1179
  Dihedral  : 13.174  85.622   2551
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  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: -0.48 (0.26), residues: 794
  helix: -0.05 (0.23), residues: 396
  sheet:  0.71 (0.65), residues: 52
  loop : -0.67 (0.30), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 473 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.029   0.003   PHE E 369 
 TYR   0.033   0.002   TYR E 385 
 ARG   0.011   0.001   ARG E 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00779 (    7)
  link_NAG-ASN         : angle       4.47900 (   21)
  hydrogen bonds       : bond        0.14004 (  325)
  hydrogen bonds       : angle       6.29074 (  917)
  SS BOND              : bond        0.00630 (    6)
  SS BOND              : angle       2.76808 (   12)
  covalent geometry    : bond        0.00530 ( 6741)
  covalent geometry    : angle       0.83966 ( 9163)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
REVERT: E  156 LEU cc_start: 0.9544 (mm) cc_final: 0.8932 (tm)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 1.7400
  time to fit residues: 133.6495
Evaluate side-chains
  51 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 59 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.3764

-------------------------------------------------------------------------------
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  34 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
E 325 GLN
** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.068635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.050493 restraints weight = 26202.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.2804 rms_B_bonded: 3.75
r_work: 0.2637 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2643
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2643 r_free = 0.2643    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2643
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   6754  Z= 0.224
  Angle     :  0.640   8.017   9196  Z= 0.323
  Chirality :  0.043   0.163    979
  Planarity :  0.005   0.047   1179
  Dihedral  :  5.187  51.104   1014
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.27 %
    Favored  : 90.87 %
  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:  0.69 (0.28), residues: 794
  helix:  0.98 (0.25), residues: 398
  sheet:  0.72 (0.67), residues: 53
  loop : -0.09 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.021   0.002   PHE E 400 
 TYR   0.018   0.001   TYR E 385 
 ARG   0.004   0.000   ARG E 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00398 (    7)
  link_NAG-ASN         : angle       3.18120 (   21)
  hydrogen bonds       : bond        0.05130 (  325)
  hydrogen bonds       : angle       4.76582 (  917)
  SS BOND              : bond        0.00500 (    6)
  SS BOND              : angle       2.24072 (   12)
  covalent geometry    : bond        0.00504 ( 6741)
  covalent geometry    : angle       0.61747 ( 9163)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9169 (ttmm)
REVERT: B  471 GLU cc_start: 0.8972 (tp30) cc_final: 0.8728 (tp30)
REVERT: E   91 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8785 (tm)
REVERT: E  249 MET cc_start: 0.8909 (ttm) cc_final: 0.8655 (mtt)
REVERT: E  360 MET cc_start: 0.9297 (ttm) cc_final: 0.9074 (ttm)
REVERT: E  408 MET cc_start: 0.9488 (mmt) cc_final: 0.9255 (mmt)
  outliers start: 6
  outliers final: 2
  residues processed: 53
  average time/residue: 1.4721
  time to fit residues: 82.1077
Evaluate side-chains
  52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  356 LYS
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  366 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0270
   chunk 66 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 44 optimal weight:    0.2980
   chunk 8 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
B 354 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
E 117 ASN
E 374 HIS
** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.070982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.052916 restraints weight = 24567.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 3.63
r_work: 0.2720 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2728
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2728
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6754  Z= 0.117
  Angle     :  0.537   6.416   9196  Z= 0.269
  Chirality :  0.040   0.136    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.774  54.057   1014
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  9.27 %
    Favored  : 89.87 %
  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:  1.00 (0.28), residues: 794
  helix:  1.38 (0.26), residues: 391
  sheet:  1.02 (0.73), residues: 43
  loop : -0.10 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.014   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00409 (    7)
  link_NAG-ASN         : angle       2.66839 (   21)
  hydrogen bonds       : bond        0.04328 (  325)
  hydrogen bonds       : angle       4.48938 (  917)
  SS BOND              : bond        0.00436 (    6)
  SS BOND              : angle       2.08702 (   12)
  covalent geometry    : bond        0.00256 ( 6741)
  covalent geometry    : angle       0.51667 ( 9163)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.711 
Fit side-chains
REVERT: B  471 GLU cc_start: 0.8968 (tp30) cc_final: 0.8746 (tp30)
REVERT: E   91 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8784 (tm)
REVERT: E  249 MET cc_start: 0.8861 (ttm) cc_final: 0.8646 (mtt)
REVERT: E  332 MET cc_start: 0.9087 (ttp) cc_final: 0.8715 (ptm)
REVERT: E  360 MET cc_start: 0.9263 (ttm) cc_final: 0.9002 (ttm)
REVERT: E  366 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8314 (ttp)
  outliers start: 6
  outliers final: 2
  residues processed: 52
  average time/residue: 1.3183
  time to fit residues: 72.3511
Evaluate side-chains
  50 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  142 LEU
Chi-restraints excluded: chain E residue  259 ILE
Chi-restraints excluded: chain E residue  366 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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  34 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
E 522 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.070323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.052114 restraints weight = 24446.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 3.67
r_work: 0.2698 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2707
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2707 r_free = 0.2707    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2707 r_free = 0.2707    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2707
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6754  Z= 0.138
  Angle     :  0.530   6.526   9196  Z= 0.267
  Chirality :  0.040   0.141    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.669  53.987   1014
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  9.56 %
    Favored  : 89.59 %
  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: 794
  helix:  1.47 (0.26), residues: 392
  sheet:  1.13 (0.75), residues: 43
  loop :  0.02 (0.31), residues: 359

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   0.016   0.001   TYR E  50 
 ARG   0.004   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00314 (    7)
  link_NAG-ASN         : angle       2.32743 (   21)
  hydrogen bonds       : bond        0.04384 (  325)
  hydrogen bonds       : angle       4.42582 (  917)
  SS BOND              : bond        0.00382 (    6)
  SS BOND              : angle       1.65771 (   12)
  covalent geometry    : bond        0.00307 ( 6741)
  covalent geometry    : angle       0.51528 ( 9163)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.782 
Fit side-chains
REVERT: E   91 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8774 (tm)
REVERT: E  249 MET cc_start: 0.8843 (ttm) cc_final: 0.8608 (mtt)
REVERT: E  332 MET cc_start: 0.9124 (ttp) cc_final: 0.8677 (ptm)
REVERT: E  360 MET cc_start: 0.9260 (ttm) cc_final: 0.9016 (ttm)
REVERT: E  366 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8339 (ttp)
  outliers start: 6
  outliers final: 1
  residues processed: 49
  average time/residue: 1.5164
  time to fit residues: 78.3220
Evaluate side-chains
  48 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  366 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
E 522 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.068912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.050034 restraints weight = 37717.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.2804 rms_B_bonded: 4.36
r_work: 0.2626 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2634 r_free = 0.2634    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2634 r_free = 0.2634    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6754  Z= 0.184
  Angle     :  0.549   7.072   9196  Z= 0.278
  Chirality :  0.042   0.147    979
  Planarity :  0.004   0.043   1179
  Dihedral  :  4.707  54.405   1014
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  9.27 %
    Favored  : 89.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.29), residues: 794
  helix:  1.49 (0.26), residues: 392
  sheet:  0.66 (0.69), residues: 53
  loop :  0.22 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.017   0.001   PHE E 369 
 TYR   0.016   0.001   TYR E 385 
 ARG   0.003   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00230 (    7)
  link_NAG-ASN         : angle       2.18622 (   21)
  hydrogen bonds       : bond        0.04631 (  325)
  hydrogen bonds       : angle       4.45321 (  917)
  SS BOND              : bond        0.00354 (    6)
  SS BOND              : angle       1.23201 (   12)
  covalent geometry    : bond        0.00416 ( 6741)
  covalent geometry    : angle       0.53844 ( 9163)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.769 
Fit side-chains
REVERT: E   55 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8158 (p)
REVERT: E   91 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8838 (tm)
REVERT: E  156 LEU cc_start: 0.9523 (mm) cc_final: 0.9102 (tm)
REVERT: E  249 MET cc_start: 0.8904 (ttm) cc_final: 0.8661 (mtt)
REVERT: E  332 MET cc_start: 0.9147 (ttp) cc_final: 0.8901 (ttm)
REVERT: E  360 MET cc_start: 0.9291 (ttm) cc_final: 0.9053 (ttm)
REVERT: E  366 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8440 (ttp)
  outliers start: 9
  outliers final: 1
  residues processed: 50
  average time/residue: 1.4431
  time to fit residues: 76.0591
Evaluate side-chains
  49 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 501 ASN
E 522 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.067874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.049911 restraints weight = 24542.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.2791 rms_B_bonded: 3.64
r_work: 0.2634 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2624
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2624 r_free = 0.2624    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2624 r_free = 0.2624    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6754  Z= 0.190
  Angle     :  0.555   7.095   9196  Z= 0.282
  Chirality :  0.042   0.146    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.750  54.778   1014
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.13 %
    Favored  : 89.02 %
  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:  1.33 (0.29), residues: 794
  helix:  1.47 (0.26), residues: 391
  sheet:  0.54 (0.69), residues: 53
  loop :  0.40 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.016   0.001   TYR E 385 
 ARG   0.004   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00214 (    7)
  link_NAG-ASN         : angle       2.14204 (   21)
  hydrogen bonds       : bond        0.04666 (  325)
  hydrogen bonds       : angle       4.47274 (  917)
  SS BOND              : bond        0.00344 (    6)
  SS BOND              : angle       1.00925 (   12)
  covalent geometry    : bond        0.00431 ( 6741)
  covalent geometry    : angle       0.54568 ( 9163)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.771 
Fit side-chains
REVERT: B  471 GLU cc_start: 0.8988 (tp30) cc_final: 0.8769 (tp30)
REVERT: E   55 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8158 (p)
REVERT: E  156 LEU cc_start: 0.9503 (mm) cc_final: 0.9106 (tm)
REVERT: E  249 MET cc_start: 0.8870 (ttm) cc_final: 0.8601 (mtt)
REVERT: E  366 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8455 (ttp)
  outliers start: 6
  outliers final: 1
  residues processed: 50
  average time/residue: 1.3506
  time to fit residues: 71.3124
Evaluate side-chains
  48 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0980
   chunk 61 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 501 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.069609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.050845 restraints weight = 39984.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 4.48
r_work: 0.2625 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2631
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2631
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6754  Z= 0.133
  Angle     :  0.523   6.416   9196  Z= 0.263
  Chirality :  0.040   0.135    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.608  55.743   1014
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  9.99 %
    Favored  : 89.02 %
  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:  1.32 (0.29), residues: 794
  helix:  1.51 (0.26), residues: 394
  sheet:  0.46 (0.70), residues: 53
  loop :  0.33 (0.32), residues: 347

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   0.013   0.001   TYR E 385 
 ARG   0.004   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00250 (    7)
  link_NAG-ASN         : angle       2.07740 (   21)
  hydrogen bonds       : bond        0.04329 (  325)
  hydrogen bonds       : angle       4.38686 (  917)
  SS BOND              : bond        0.00286 (    6)
  SS BOND              : angle       0.83066 (   12)
  covalent geometry    : bond        0.00299 ( 6741)
  covalent geometry    : angle       0.51309 ( 9163)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.666 
Fit side-chains
REVERT: B  471 GLU cc_start: 0.9084 (tp30) cc_final: 0.8834 (tp30)
REVERT: E   55 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8234 (p)
REVERT: E   91 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8807 (tm)
REVERT: E  152 MET cc_start: 0.8790 (mmm) cc_final: 0.8588 (tpt)
REVERT: E  156 LEU cc_start: 0.9499 (mm) cc_final: 0.9107 (tm)
REVERT: E  249 MET cc_start: 0.8882 (ttm) cc_final: 0.8631 (mtt)
REVERT: E  332 MET cc_start: 0.9044 (ttp) cc_final: 0.8739 (ttm)
REVERT: E  360 MET cc_start: 0.9293 (ttm) cc_final: 0.9037 (ttm)
REVERT: E  366 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8423 (ttp)
REVERT: E  480 MET cc_start: 0.9134 (mtp) cc_final: 0.8849 (mtm)
  outliers start: 7
  outliers final: 2
  residues processed: 51
  average time/residue: 1.4610
  time to fit residues: 78.4581
Evaluate side-chains
  51 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 3 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 76 optimal weight:    0.4980
   chunk 5 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 60 optimal weight:    0.3980
   chunk 54 optimal weight:    0.1980
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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  34 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 522 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 = 0.3277 r_free = 0.3277 target = 0.070515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.051880 restraints weight = 33951.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 4.24
r_work: 0.2665 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2666 r_free = 0.2666    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6754  Z= 0.117
  Angle     :  0.506   6.684   9196  Z= 0.255
  Chirality :  0.040   0.133    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.480  56.026   1014
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.56 %
    Favored  : 88.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.29), residues: 794
  helix:  1.62 (0.26), residues: 393
  sheet:  0.85 (0.78), residues: 43
  loop :  0.31 (0.32), residues: 358

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   0.013   0.001   TYR E 385 
 ARG   0.003   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00262 (    7)
  link_NAG-ASN         : angle       1.96277 (   21)
  hydrogen bonds       : bond        0.04104 (  325)
  hydrogen bonds       : angle       4.30944 (  917)
  SS BOND              : bond        0.00269 (    6)
  SS BOND              : angle       0.78210 (   12)
  covalent geometry    : bond        0.00259 ( 6741)
  covalent geometry    : angle       0.49783 ( 9163)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.670 
Fit side-chains
REVERT: E   55 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8233 (p)
REVERT: E   91 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8796 (tm)
REVERT: E  156 LEU cc_start: 0.9510 (mm) cc_final: 0.9124 (tm)
REVERT: E  249 MET cc_start: 0.8811 (ttm) cc_final: 0.8555 (mtt)
REVERT: E  332 MET cc_start: 0.9018 (ttp) cc_final: 0.8731 (ttm)
REVERT: E  360 MET cc_start: 0.9307 (ttm) cc_final: 0.9039 (ttm)
REVERT: E  366 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8331 (ttp)
  outliers start: 5
  outliers final: 2
  residues processed: 48
  average time/residue: 1.4702
  time to fit residues: 74.3125
Evaluate side-chains
  50 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain E residue  366 MET
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 26 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0370
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0030
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 31 optimal weight:    7.9990
   overall best weight:    0.3268

-------------------------------------------------------------------------------
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  34 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 522 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 = 0.3317 r_free = 0.3317 target = 0.071907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.053973 restraints weight = 22403.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 3.55
r_work: 0.2750 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6754  Z= 0.104
  Angle     :  0.497   7.544   9196  Z= 0.249
  Chirality :  0.039   0.129    979
  Planarity :  0.004   0.043   1179
  Dihedral  :  4.358  56.479   1014
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.98 %
    Favored  : 88.30 %
  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:  1.52 (0.29), residues: 794
  helix:  1.67 (0.26), residues: 395
  sheet:  0.84 (0.78), residues: 43
  loop :  0.40 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00264 (    7)
  link_NAG-ASN         : angle       1.88347 (   21)
  hydrogen bonds       : bond        0.03884 (  325)
  hydrogen bonds       : angle       4.23369 (  917)
  SS BOND              : bond        0.00243 (    6)
  SS BOND              : angle       0.66816 (   12)
  covalent geometry    : bond        0.00227 ( 6741)
  covalent geometry    : angle       0.48933 ( 9163)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.649 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8312 (p)
REVERT: E   63 ASN cc_start: 0.9142 (m-40) cc_final: 0.8843 (m110)
REVERT: E   91 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8795 (tm)
REVERT: E  156 LEU cc_start: 0.9517 (mm) cc_final: 0.9150 (tm)
REVERT: E  249 MET cc_start: 0.8787 (ttm) cc_final: 0.8552 (mtt)
REVERT: E  332 MET cc_start: 0.8951 (ttp) cc_final: 0.8669 (ptm)
REVERT: E  360 MET cc_start: 0.9193 (ttm) cc_final: 0.8941 (ttm)
REVERT: E  366 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8262 (ttp)
  outliers start: 5
  outliers final: 2
  residues processed: 53
  average time/residue: 1.3575
  time to fit residues: 75.8558
Evaluate side-chains
  52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain E residue  366 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 69 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 54 optimal weight:    0.4980
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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  34 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
E 508 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.070160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.052393 restraints weight = 26885.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 3.78
r_work: 0.2709 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6754  Z= 0.127
  Angle     :  0.520   7.421   9196  Z= 0.263
  Chirality :  0.040   0.134    979
  Planarity :  0.004   0.043   1179
  Dihedral  :  4.384  55.890   1014
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.26 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 11.41 %
    Favored  : 88.02 %
  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:  1.58 (0.29), residues: 794
  helix:  1.71 (0.26), residues: 395
  sheet:  0.86 (0.78), residues: 43
  loop :  0.44 (0.32), residues: 356

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   0.015   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.002   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    7)
  link_NAG-ASN         : angle       1.85620 (   21)
  hydrogen bonds       : bond        0.04049 (  325)
  hydrogen bonds       : angle       4.23683 (  917)
  SS BOND              : bond        0.00256 (    6)
  SS BOND              : angle       0.70630 (   12)
  covalent geometry    : bond        0.00285 ( 6741)
  covalent geometry    : angle       0.51268 ( 9163)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
REVERT: E   55 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8223 (p)
REVERT: E   63 ASN cc_start: 0.9140 (m-40) cc_final: 0.8844 (m110)
REVERT: E   91 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8785 (tm)
REVERT: E  156 LEU cc_start: 0.9524 (mm) cc_final: 0.9145 (tm)
REVERT: E  249 MET cc_start: 0.8811 (ttm) cc_final: 0.8555 (mtt)
REVERT: E  366 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8236 (ttp)
  outliers start: 4
  outliers final: 2
  residues processed: 51
  average time/residue: 1.4145
  time to fit residues: 76.2772
Evaluate side-chains
  52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  339 VAL
Chi-restraints excluded: chain E residue  366 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.3980
   chunk 59 optimal weight:    0.0970
   chunk 76 optimal weight:    0.7980
   chunk 61 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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  34 HIS    A ** 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 = 0.3301 r_free = 0.3301 target = 0.071143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.052556 restraints weight = 31660.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 4.10
r_work: 0.2700 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6754  Z= 0.118
  Angle     :  0.514   7.296   9196  Z= 0.260
  Chirality :  0.040   0.132    979
  Planarity :  0.004   0.043   1179
  Dihedral  :  4.393  56.044   1014
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 11.41 %
    Favored  : 88.02 %
  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:  1.57 (0.29), residues: 794
  helix:  1.71 (0.26), residues: 395
  sheet:  0.83 (0.78), residues: 43
  loop :  0.42 (0.32), residues: 356

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   0.012   0.001   TYR E 385 
 ARG   0.001   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00230 (    7)
  link_NAG-ASN         : angle       1.83799 (   21)
  hydrogen bonds       : bond        0.04028 (  325)
  hydrogen bonds       : angle       4.23672 (  917)
  SS BOND              : bond        0.00253 (    6)
  SS BOND              : angle       0.70221 (   12)
  covalent geometry    : bond        0.00263 ( 6741)
  covalent geometry    : angle       0.50656 ( 9163)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4884.41 seconds
wall clock time: 84 minutes 24.18 seconds (5064.18 seconds total)