Starting phenix.real_space_refine
on Tue Mar  3 15:38:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sxy_25510/03_2026/7sxy_25510.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sxy_25510/03_2026/7sxy_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sxy_25510/03_2026/7sxy_25510.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sxy_25510/03_2026/7sxy_25510.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sxy_25510/03_2026/7sxy_25510.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sxy_25510/03_2026/7sxy_25510.map"
  }
  resolution = 2.79
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.42, per 1000 atoms: 0.37
  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: 0.65
  Conformation dependent library (CDL) restraints added in 417.0 milliseconds
  

  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: 0.22
  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: 0.96

  Time building geometry restraints manager: 0.83 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:             4.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.480
  Find NCS groups from input model:        0.030
  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:6.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.560
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.011   0.001   ARG E 460 
 TYR   0.033   0.002   TYR E 385 
 PHE   0.029   0.003   PHE E 369 
 TRP   0.020   0.002   TRP E 473 
 HIS   0.004   0.001   HIS E 374 

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

*********************** 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  : 0.256 
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: 0.7016
  time to fit residues: 52.7940
Evaluate side-chains
  50 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3291 r_free = 0.3291 target = 0.070414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.053147 restraints weight = 17469.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 3.10
r_work: 0.2734 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6754  Z= 0.164
  Angle     :  0.605   7.315   9196  Z= 0.304
  Chirality :  0.042   0.154    979
  Planarity :  0.005   0.046   1179
  Dihedral  :  5.059  51.562   1014
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  7.85 %
    Favored  : 91.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.28), residues: 794
  helix:  1.00 (0.25), residues: 399
  sheet:  0.69 (0.66), residues: 53
  loop : -0.19 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 219 
 TYR   0.015   0.001   TYR E 385 
 PHE   0.017   0.001   PHE E 369 
 TRP   0.020   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6741)
  covalent geometry    : angle       0.58221 ( 9163)
  SS BOND              : bond        0.00467 (    6)
  SS BOND              : angle       2.28311 (   12)
  hydrogen bonds       : bond        0.04837 (  325)
  hydrogen bonds       : angle       4.71236 (  917)
  link_NAG-ASN         : bond        0.00433 (    7)
  link_NAG-ASN         : angle       3.08846 (   21)

*********************** 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
  57 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: B  471 GLU cc_start: 0.8845 (tp30) cc_final: 0.8617 (tp30)
REVERT: E   91 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8759 (tm)
REVERT: E  249 MET cc_start: 0.8880 (ttm) cc_final: 0.8643 (mtt)
REVERT: E  360 MET cc_start: 0.9257 (ttm) cc_final: 0.9040 (ttm)
REVERT: E  366 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8257 (ttp)
REVERT: E  480 MET cc_start: 0.9178 (mtp) cc_final: 0.8946 (mtm)
  outliers start: 6
  outliers final: 1
  residues processed: 52
  average time/residue: 0.7047
  time to fit residues: 38.3580
Evaluate side-chains
  51 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 48
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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  366 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 374 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.069690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.051720 restraints weight = 21269.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 3.43
r_work: 0.2693 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2702
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6754  Z= 0.166
  Angle     :  0.564   7.231   9196  Z= 0.285
  Chirality :  0.041   0.149    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.863  53.273   1014
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.27 %
    Favored  : 90.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.29), residues: 794
  helix:  1.32 (0.26), residues: 397
  sheet:  0.66 (0.68), residues: 53
  loop :  0.09 (0.32), residues: 344

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 6741)
  covalent geometry    : angle       0.54568 ( 9163)
  SS BOND              : bond        0.00464 (    6)
  SS BOND              : angle       2.06064 (   12)
  hydrogen bonds       : bond        0.04694 (  325)
  hydrogen bonds       : angle       4.51142 (  917)
  link_NAG-ASN         : bond        0.00359 (    7)
  link_NAG-ASN         : angle       2.64117 (   21)

*********************** 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
  53 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.254 
Fit side-chains
REVERT: B  471 GLU cc_start: 0.8972 (tp30) cc_final: 0.8756 (tp30)
REVERT: E   91 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8804 (tm)
REVERT: E  249 MET cc_start: 0.8879 (ttm) cc_final: 0.8660 (mtt)
REVERT: E  332 MET cc_start: 0.9121 (ttp) cc_final: 0.8690 (ptm)
REVERT: E  360 MET cc_start: 0.9254 (ttm) cc_final: 0.9005 (ttm)
REVERT: E  366 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8357 (ttp)
  outliers start: 5
  outliers final: 2
  residues processed: 50
  average time/residue: 0.6977
  time to fit residues: 36.6709
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  : 0.271 
-------------------------------------------------------------------------------
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 10 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 58 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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.070305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.051754 restraints weight = 31347.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 4.05
r_work: 0.2679 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    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 = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.1873

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= 0.130
  Angle     :  0.526   6.476   9196  Z= 0.264
  Chirality :  0.040   0.138    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.660  54.474   1014
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  9.13 %
    Favored  : 90.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.29), residues: 794
  helix:  1.49 (0.26), residues: 391
  sheet:  0.75 (0.69), residues: 53
  loop :  0.05 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 403 
 TYR   0.014   0.001   TYR E 385 
 PHE   0.016   0.001   PHE E 369 
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6741)
  covalent geometry    : angle       0.51192 ( 9163)
  SS BOND              : bond        0.00379 (    6)
  SS BOND              : angle       1.62454 (   12)
  hydrogen bonds       : bond        0.04357 (  325)
  hydrogen bonds       : angle       4.40867 (  917)
  link_NAG-ASN         : bond        0.00329 (    7)
  link_NAG-ASN         : angle       2.32771 (   21)

*********************** 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
  50 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.261 
Fit side-chains
REVERT: E   91 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8766 (tm)
REVERT: E  249 MET cc_start: 0.8876 (ttm) cc_final: 0.8659 (mtt)
REVERT: E  332 MET cc_start: 0.9133 (ttp) cc_final: 0.8901 (ttm)
REVERT: E  360 MET cc_start: 0.9276 (ttm) cc_final: 0.9050 (ttm)
REVERT: E  366 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8359 (ttp)
  outliers start: 5
  outliers final: 0
  residues processed: 47
  average time/residue: 0.6982
  time to fit residues: 34.4251
Evaluate side-chains
  46 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 0 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3270 r_free = 0.3270 target = 0.069508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.051645 restraints weight = 20928.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 3.40
r_work: 0.2693 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    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 = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6754  Z= 0.159
  Angle     :  0.539   6.858   9196  Z= 0.271
  Chirality :  0.041   0.143    979
  Planarity :  0.004   0.043   1179
  Dihedral  :  4.655  54.695   1014
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.13 %
    Favored  : 89.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.29), residues: 794
  helix:  1.55 (0.26), residues: 390
  sheet:  0.75 (0.70), residues: 53
  loop :  0.25 (0.32), residues: 351

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6741)
  covalent geometry    : angle       0.52816 ( 9163)
  SS BOND              : bond        0.00331 (    6)
  SS BOND              : angle       1.13894 (   12)
  hydrogen bonds       : bond        0.04507 (  325)
  hydrogen bonds       : angle       4.39740 (  917)
  link_NAG-ASN         : bond        0.00258 (    7)
  link_NAG-ASN         : angle       2.16343 (   21)

*********************** 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
  52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.277 
Fit side-chains
REVERT: B  471 GLU cc_start: 0.8963 (tp30) cc_final: 0.8742 (tp30)
REVERT: E   55 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8182 (p)
REVERT: E   91 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8800 (tm)
REVERT: E  249 MET cc_start: 0.8883 (ttm) cc_final: 0.8663 (mtt)
REVERT: E  360 MET cc_start: 0.9238 (ttm) cc_final: 0.9017 (ttm)
REVERT: E  366 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8371 (ttp)
  outliers start: 8
  outliers final: 1
  residues processed: 47
  average time/residue: 0.7650
  time to fit residues: 37.6259
Evaluate side-chains
  47 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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 18 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 43 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3271 r_free = 0.3271 target = 0.069570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.051041 restraints weight = 31062.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.2831 rms_B_bonded: 4.03
r_work: 0.2661 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    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 = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.2043

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= 0.149
  Angle     :  0.524   6.592   9196  Z= 0.264
  Chirality :  0.040   0.139    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.625  55.347   1014
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  8.70 %
    Favored  : 90.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.29), residues: 794
  helix:  1.52 (0.26), residues: 393
  sheet:  0.71 (0.71), residues: 53
  loop :  0.32 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 403 
 TYR   0.014   0.001   TYR E 385 
 PHE   0.015   0.001   PHE E 369 
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6741)
  covalent geometry    : angle       0.51456 ( 9163)
  SS BOND              : bond        0.00306 (    6)
  SS BOND              : angle       0.91802 (   12)
  hydrogen bonds       : bond        0.04408 (  325)
  hydrogen bonds       : angle       4.37234 (  917)
  link_NAG-ASN         : bond        0.00241 (    7)
  link_NAG-ASN         : angle       2.06418 (   21)

*********************** 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
  56 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.264 
Fit side-chains
REVERT: E   55 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8254 (p)
REVERT: E   91 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8805 (tm)
REVERT: E  156 LEU cc_start: 0.9519 (mm) cc_final: 0.9111 (tm)
REVERT: E  249 MET cc_start: 0.8906 (ttm) cc_final: 0.8679 (mtt)
REVERT: E  332 MET cc_start: 0.9090 (ttp) cc_final: 0.8799 (ttm)
REVERT: E  360 MET cc_start: 0.9269 (ttm) cc_final: 0.9045 (ttm)
REVERT: E  366 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8392 (ttp)
  outliers start: 9
  outliers final: 1
  residues processed: 52
  average time/residue: 0.7148
  time to fit residues: 39.1571
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  : 0.274 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3255 r_free = 0.3255 target = 0.069467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.051071 restraints weight = 31427.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 4.04
r_work: 0.2643 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6754  Z= 0.148
  Angle     :  0.529   6.934   9196  Z= 0.266
  Chirality :  0.040   0.138    979
  Planarity :  0.004   0.043   1179
  Dihedral  :  4.591  55.497   1014
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  9.84 %
    Favored  : 89.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.29), residues: 794
  helix:  1.57 (0.26), residues: 393
  sheet:  0.66 (0.71), residues: 53
  loop :  0.32 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 403 
 TYR   0.014   0.001   TYR E 385 
 PHE   0.015   0.001   PHE E 369 
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6741)
  covalent geometry    : angle       0.52019 ( 9163)
  SS BOND              : bond        0.00297 (    6)
  SS BOND              : angle       0.86694 (   12)
  hydrogen bonds       : bond        0.04390 (  325)
  hydrogen bonds       : angle       4.35363 (  917)
  link_NAG-ASN         : bond        0.00228 (    7)
  link_NAG-ASN         : angle       2.01317 (   21)

*********************** 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
  52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.259 
Fit side-chains
REVERT: B  471 GLU cc_start: 0.8974 (tp30) cc_final: 0.8760 (tp30)
REVERT: E   55 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8204 (p)
REVERT: E   91 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8779 (tm)
REVERT: E  156 LEU cc_start: 0.9503 (mm) cc_final: 0.9104 (tm)
REVERT: E  249 MET cc_start: 0.8875 (ttm) cc_final: 0.8619 (mtt)
REVERT: E  360 MET cc_start: 0.9280 (ttm) cc_final: 0.9036 (ttm)
REVERT: E  366 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8395 (ttp)
  outliers start: 6
  outliers final: 3
  residues processed: 49
  average time/residue: 0.7247
  time to fit residues: 37.2677
Evaluate side-chains
  50 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
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
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 33 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0970
   chunk 39 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.3262 r_free = 0.3262 target = 0.069820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.052513 restraints weight = 17597.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 3.15
r_work: 0.2706 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    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 = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2118

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= 0.135
  Angle     :  0.519   6.636   9196  Z= 0.261
  Chirality :  0.040   0.135    979
  Planarity :  0.004   0.043   1179
  Dihedral  :  4.556  55.798   1014
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.76
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.29), residues: 794
  helix:  1.59 (0.26), residues: 393
  sheet:  0.63 (0.71), residues: 53
  loop :  0.32 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 403 
 TYR   0.014   0.001   TYR E 385 
 PHE   0.015   0.001   PHE E 369 
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6741)
  covalent geometry    : angle       0.51046 ( 9163)
  SS BOND              : bond        0.00281 (    6)
  SS BOND              : angle       0.80651 (   12)
  hydrogen bonds       : bond        0.04312 (  325)
  hydrogen bonds       : angle       4.32529 (  917)
  link_NAG-ASN         : bond        0.00234 (    7)
  link_NAG-ASN         : angle       1.97488 (   21)

*********************** 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
  53 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.306 
Fit side-chains
REVERT: E   55 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8237 (p)
REVERT: E   91 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8766 (tm)
REVERT: E  156 LEU cc_start: 0.9509 (mm) cc_final: 0.9127 (tm)
REVERT: E  249 MET cc_start: 0.8838 (ttm) cc_final: 0.8586 (mtt)
REVERT: E  360 MET cc_start: 0.9256 (ttm) cc_final: 0.9018 (ttm)
REVERT: E  366 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8358 (ttp)
REVERT: E  480 MET cc_start: 0.9102 (mtp) cc_final: 0.8772 (mtm)
  outliers start: 6
  outliers final: 3
  residues processed: 51
  average time/residue: 0.6952
  time to fit residues: 37.2509
Evaluate side-chains
  52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
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
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 0 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0050
   chunk 9 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.0998

-------------------------------------------------------------------------------
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 = 0.3243 r_free = 0.3243 target = 0.068816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.050329 restraints weight = 31843.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 4.07
r_work: 0.2626 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    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 = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6754  Z= 0.183
  Angle     :  0.547   6.805   9196  Z= 0.277
  Chirality :  0.041   0.143    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.616  55.195   1014
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.84 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.29), residues: 794
  helix:  1.60 (0.26), residues: 392
  sheet:  0.61 (0.71), residues: 53
  loop :  0.44 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 403 
 TYR   0.016   0.001   TYR E 385 
 PHE   0.016   0.001   PHE E 369 
 TRP   0.015   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 6741)
  covalent geometry    : angle       0.53862 ( 9163)
  SS BOND              : bond        0.00317 (    6)
  SS BOND              : angle       0.87577 (   12)
  hydrogen bonds       : bond        0.04534 (  325)
  hydrogen bonds       : angle       4.35570 (  917)
  link_NAG-ASN         : bond        0.00185 (    7)
  link_NAG-ASN         : angle       1.99601 (   21)

*********************** 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
  51 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.224 
Fit side-chains
REVERT: E   55 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8211 (p)
REVERT: E   91 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8827 (tm)
REVERT: E  156 LEU cc_start: 0.9510 (mm) cc_final: 0.9129 (tm)
REVERT: E  249 MET cc_start: 0.8892 (ttm) cc_final: 0.8633 (mtt)
REVERT: E  360 MET cc_start: 0.9289 (ttm) cc_final: 0.9036 (ttm)
REVERT: E  366 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8417 (ttp)
  outliers start: 5
  outliers final: 3
  residues processed: 49
  average time/residue: 0.7331
  time to fit residues: 37.7078
Evaluate side-chains
  52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3249 r_free = 0.3249 target = 0.069166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.050785 restraints weight = 28465.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.2813 rms_B_bonded: 3.90
r_work: 0.2642 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2647 r_free = 0.2647    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6754  Z= 0.156
  Angle     :  0.541   6.599   9196  Z= 0.273
  Chirality :  0.041   0.138    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.610  55.604   1014
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.56 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.29), residues: 794
  helix:  1.59 (0.26), residues: 392
  sheet:  0.51 (0.71), residues: 53
  loop :  0.45 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 245 
 TYR   0.014   0.001   TYR E 385 
 PHE   0.016   0.001   PHE E 369 
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6741)
  covalent geometry    : angle       0.53224 ( 9163)
  SS BOND              : bond        0.00306 (    6)
  SS BOND              : angle       0.85205 (   12)
  hydrogen bonds       : bond        0.04451 (  325)
  hydrogen bonds       : angle       4.34486 (  917)
  link_NAG-ASN         : bond        0.00216 (    7)
  link_NAG-ASN         : angle       1.99148 (   21)

********************** 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: 6
    poor density    : 46
  time to evaluate  : 0.280 
Fit side-chains
REVERT: E   55 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8210 (p)
REVERT: E   91 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8791 (tm)
REVERT: E  156 LEU cc_start: 0.9502 (mm) cc_final: 0.9115 (tm)
REVERT: E  249 MET cc_start: 0.8877 (ttm) cc_final: 0.8620 (mtt)
REVERT: E  360 MET cc_start: 0.9278 (ttm) cc_final: 0.9029 (ttm)
REVERT: E  366 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8416 (ttp)
  outliers start: 6
  outliers final: 3
  residues processed: 49
  average time/residue: 0.7217
  time to fit residues: 37.2001
Evaluate side-chains
  52 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain E residue  474 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0870
   chunk 65 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0060
   chunk 38 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.5374

-------------------------------------------------------------------------------
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 = 0.3265 r_free = 0.3265 target = 0.069905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.052118 restraints weight = 21666.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 3.48
r_work: 0.2688 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    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 = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6754  Z= 0.124
  Angle     :  0.525   6.348   9196  Z= 0.264
  Chirality :  0.040   0.132    979
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.550  56.089   1014
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.70 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.29), residues: 794
  helix:  1.62 (0.26), residues: 392
  sheet:  0.44 (0.71), residues: 53
  loop :  0.38 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 403 
 TYR   0.013   0.001   TYR E 385 
 PHE   0.015   0.001   PHE E 369 
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6741)
  covalent geometry    : angle       0.51657 ( 9163)
  SS BOND              : bond        0.00284 (    6)
  SS BOND              : angle       0.79245 (   12)
  hydrogen bonds       : bond        0.04275 (  325)
  hydrogen bonds       : angle       4.31087 (  917)
  link_NAG-ASN         : bond        0.00257 (    7)
  link_NAG-ASN         : angle       1.97654 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2416.96 seconds
wall clock time: 41 minutes 58.37 seconds (2518.37 seconds total)