Starting phenix.real_space_refine
on Thu Jul 24 19:33:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fdh_31543/07_2025/7fdh_31543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fdh_31543/07_2025/7fdh_31543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fdh_31543/07_2025/7fdh_31543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fdh_31543/07_2025/7fdh_31543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fdh_31543/07_2025/7fdh_31543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fdh_31543/07_2025/7fdh_31543.cif"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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    4150      2.51       5
     N    1069      2.21       5
     O    1232      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6488
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4877
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
      Conformer: "B"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
          bond proxies already assigned to first conformer: 4998
    Chain: "E"
      Number of atoms: 1541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1541
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      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
  Time building chain proxies: 6.87, per 1000 atoms: 1.06
  Number of scatterers: 6488
  At special positions: 0
  Unit cell: (122.72, 78, 76.96, 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    1232      8.00
     N    1069      7.00
     C    4150      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 546 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 703 " - " ASN A 322 "
      " NAG A 704 " - " ASN A  53 "
      " NAG E 601 " - " ASN E 343 "
  Time building additional restraints: 1.77
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      57.0% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.872A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.565A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.609A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.560A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.779A  pdb=" N   VAL A 172 " --> pdb=" O   TRP A 168 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.812A  pdb=" N   ASN A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 218 through 252
      removed outlier: 3.756A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 299
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.588A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.974A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.846A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.962A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 446
    Processing helix  chain 'A' and resid 448 through 465
      removed outlier: 4.211A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.963A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS A 481 " --> pdb=" O   TRP A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 509
    Processing helix  chain 'A' and resid 513 through 533
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.970A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.808A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'E' and resid 337 through 343
      removed outlier: 3.955A  pdb=" N   VAL E 341 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 349 through 353
    Processing helix  chain 'E' and resid 365 through 370
    Processing helix  chain 'E' and resid 385 through 390
      removed outlier: 3.531A  pdb=" N   LEU E 390 " --> pdb=" O   LEU E 387 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 404 through 410
    Processing helix  chain 'E' and resid 416 through 421
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.960A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 5.692A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358
    Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474

    320 hydrogen bonds defined for protein.
    893 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: 1.68

  Time building geometry restraints manager: 2.09 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2079
        1.35 -     1.47: 1767
        1.47 -     1.59: 2768
        1.59 -     1.71: 0
        1.71 -     1.84: 58
  Bond restraints: 6672
  Sorted by residual:
  bond pdb=" C1  NAG E 601 "
       pdb=" O5  NAG E 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.24e+00
  bond pdb=" C1  NAG A 704 "
       pdb=" O5  NAG A 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.90e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.74e+00
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.61e+00
  bond pdb=" C5  NAG E 601 "
       pdb=" O5  NAG E 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.438 -0.025 2.00e-02 2.50e+03 1.51e+00
  ... (remaining 6667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 8902
        2.20 -     4.39: 150
        4.39 -     6.59: 15
        6.59 -     8.79: 3
        8.79 -    10.98: 1
  Bond angle restraints: 9071
  Sorted by residual:
  angle pdb=" CA  CYS A 141 "
        pdb=" CB  CYS A 141 "
        pdb=" SG  CYS A 141 "
      ideal   model   delta    sigma   weight residual
     114.40  125.38  -10.98 2.30e+00 1.89e-01 2.28e+01
  angle pdb=" N   CYS A 141 "
        pdb=" CA  CYS A 141 "
        pdb=" C   CYS A 141 "
      ideal   model   delta    sigma   weight residual
     108.96  115.21   -6.25 1.49e+00 4.50e-01 1.76e+01
  angle pdb=" N   CYS E 379 "
        pdb=" CA  CYS E 379 "
        pdb=" C   CYS E 379 "
      ideal   model   delta    sigma   weight residual
     108.60  114.00   -5.40 1.46e+00 4.69e-01 1.37e+01
  angle pdb=" CA  CYS E 379 "
        pdb=" CB  CYS E 379 "
        pdb=" SG  CYS E 379 "
      ideal   model   delta    sigma   weight residual
     114.40  121.73   -7.33 2.30e+00 1.89e-01 1.01e+01
  angle pdb=" CA  CYS A 133 "
        pdb=" CB  CYS A 133 "
        pdb=" SG  CYS A 133 "
      ideal   model   delta    sigma   weight residual
     114.40  121.68   -7.28 2.30e+00 1.89e-01 1.00e+01
  ... (remaining 9066 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 3552
       17.59 -    35.19: 350
       35.19 -    52.78: 73
       52.78 -    70.37: 12
       70.37 -    87.96: 10
  Dihedral angle restraints: 3997
    sinusoidal: 1672
      harmonic: 2325
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   11.10   81.90     1      1.00e+01 1.00e-02 8.25e+01
  dihedral pdb=" CA  CYS A 141 "
           pdb=" C   CYS A 141 "
           pdb=" N   LEU A 142 "
           pdb=" CA  LEU A 142 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.46  -26.54     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CB  CYS E 379 "
           pdb=" SG  CYS E 379 "
           pdb=" SG  CYS E 432 "
           pdb=" CB  CYS E 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.66   41.34     1      1.00e+01 1.00e-02 2.39e+01
  ... (remaining 3994 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 862
       0.078 -    0.156: 97
       0.156 -    0.234: 1
       0.234 -    0.312: 1
       0.312 -    0.390: 1
  Chirality restraints: 962
  Sorted by residual:
  chirality pdb=" C1  NAG E 601 "
            pdb=" ND2 ASN E 343 "
            pdb=" C2  NAG E 601 "
            pdb=" O5  NAG E 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.81e+00
  chirality pdb=" CA  CYS A 141 "
            pdb=" N   CYS A 141 "
            pdb=" C   CYS A 141 "
            pdb=" CB  CYS A 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CA  ASN E 343 "
            pdb=" N   ASN E 343 "
            pdb=" C   ASN E 343 "
            pdb=" CB  ASN E 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.59e-01
  ... (remaining 959 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 145 "   -0.034 5.00e-02 4.00e+02   5.10e-02 4.17e+00
        pdb=" N   PRO A 146 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A  33 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.07e+00
        pdb=" C   ASN A  33 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ASN A  33 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   HIS A  34 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 582 "    0.028 5.00e-02 4.00e+02   4.18e-02 2.80e+00
        pdb=" N   PRO A 583 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 196
        2.70 -     3.25: 6959
        3.25 -     3.80: 10455
        3.80 -     4.35: 13483
        4.35 -     4.90: 22150
  Nonbonded interactions: 53243
  Sorted by model distance:
  nonbonded pdb=" OG  SER E 438 "
            pdb=" OD2 ASP E 442 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" O   VAL E 367 "
            pdb=" OG  SER E 371 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" NE2 GLN A 221 "
            pdb=" OD1 ASP A 225 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OG  SER A 511 "
            pdb=" NH2 ARG A 514 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" OG  SER E 349 "
            pdb=" O   LEU E 452 "
     model   vdw
     2.236 3.040
  ... (remaining 53238 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.540
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6684  Z= 0.206
  Angle     :  0.751  10.983   9100  Z= 0.430
  Chirality :  0.048   0.390    962
  Planarity :  0.005   0.051   1170
  Dihedral  : 14.493  87.964   2486
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.88 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -2.91 (0.25), residues: 788
  helix: -1.53 (0.22), residues: 377
  sheet: -0.84 (0.69), residues: 50
  loop : -2.49 (0.27), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 473 
 HIS   0.004   0.001   HIS A 540 
 PHE   0.015   0.002   PHE A 314 
 TYR   0.021   0.002   TYR E 453 
 ARG   0.003   0.001   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00866 (    5)
  link_NAG-ASN         : angle       2.30054 (   15)
  hydrogen bonds       : bond        0.14443 (  320)
  hydrogen bonds       : angle       6.54927 (  893)
  SS BOND              : bond        0.00425 (    7)
  SS BOND              : angle       3.24811 (   14)
  covalent geometry    : bond        0.00423 ( 6672)
  covalent geometry    : angle       0.73489 ( 9071)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8102 (m-40) cc_final: 0.7867 (t0)
REVERT: A   98 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7859 (tp-100)
REVERT: A  123 MET cc_start: 0.7787 (mtm) cc_final: 0.7464 (mtt)
REVERT: A  165 TRP cc_start: 0.7254 (t60) cc_final: 0.5965 (t60)
REVERT: A  455 MET cc_start: 0.8600 (tmm) cc_final: 0.8285 (tmm)
REVERT: A  478 TRP cc_start: 0.7962 (m100) cc_final: 0.7587 (m100)
REVERT: A  497 TYR cc_start: 0.7564 (m-80) cc_final: 0.6574 (m-80)
REVERT: A  505 HIS cc_start: 0.7573 (m90) cc_final: 0.7157 (m-70)
REVERT: E  366 SER cc_start: 0.8329 (m) cc_final: 0.8047 (p)
REVERT: E  396 TYR cc_start: 0.7613 (m-80) cc_final: 0.6939 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 125
  average time/residue: 0.2162
  time to fit residues: 34.8391
Evaluate side-chains
  84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 59 optimal weight:    0.1980
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A 221 GLN
A 239 HIS
A 290 ASN
** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 526 GLN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN
E 334 ASN
E 388 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.109016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.083280 restraints weight = 26553.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.087560 restraints weight = 10651.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.088845 restraints weight = 5350.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3380
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3380
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6684  Z= 0.143
  Angle     :  0.649   9.560   9100  Z= 0.329
  Chirality :  0.046   0.283    962
  Planarity :  0.005   0.062   1170
  Dihedral  :  5.327  33.710    968
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.79 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.76 (0.28), residues: 788
  helix:  0.20 (0.25), residues: 387
  sheet: -0.24 (0.72), residues: 51
  loop : -1.30 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 168 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.013   0.001   PHE E 392 
 TYR   0.020   0.002   TYR A 183 
 ARG   0.005   0.001   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00572 (    5)
  link_NAG-ASN         : angle       1.55009 (   15)
  hydrogen bonds       : bond        0.04955 (  320)
  hydrogen bonds       : angle       4.95424 (  893)
  SS BOND              : bond        0.00625 (    7)
  SS BOND              : angle       1.71910 (   14)
  covalent geometry    : bond        0.00308 ( 6672)
  covalent geometry    : angle       0.64351 ( 9071)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8153 (m-40) cc_final: 0.7866 (t0)
REVERT: A  123 MET cc_start: 0.7928 (mtm) cc_final: 0.7535 (mtt)
REVERT: A  165 TRP cc_start: 0.7328 (t60) cc_final: 0.6380 (t60)
REVERT: A  222 LEU cc_start: 0.8491 (tp) cc_final: 0.8265 (tp)
REVERT: A  249 MET cc_start: 0.8022 (mmm) cc_final: 0.7768 (mmm)
REVERT: A  455 MET cc_start: 0.8505 (tmm) cc_final: 0.8213 (tmm)
REVERT: A  497 TYR cc_start: 0.8071 (m-80) cc_final: 0.6917 (m-80)
REVERT: A  505 HIS cc_start: 0.7577 (m90) cc_final: 0.7168 (m-70)
REVERT: A  557 MET cc_start: 0.9187 (tmm) cc_final: 0.8737 (tmm)
REVERT: E  340 GLU cc_start: 0.8064 (pt0) cc_final: 0.7442 (mm-30)
REVERT: E  392 PHE cc_start: 0.8610 (m-80) cc_final: 0.8304 (m-10)
REVERT: E  450 ASN cc_start: 0.8438 (m110) cc_final: 0.8210 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 112
  average time/residue: 0.1993
  time to fit residues: 29.2274
Evaluate side-chains
  89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 21 optimal weight:    0.6980
   chunk 73 optimal weight:    0.1980
   chunk 15 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 ASN
A 599 ASN
E 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.110325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.083948 restraints weight = 19206.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.087238 restraints weight = 8801.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.089429 restraints weight = 5459.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3403
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3403 r_free = 0.3403    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3403 r_free = 0.3403    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3403
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6684  Z= 0.133
  Angle     :  0.616   8.909   9100  Z= 0.311
  Chirality :  0.044   0.247    962
  Planarity :  0.004   0.040   1170
  Dihedral  :  4.834  29.524    967
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.66 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.29), residues: 788
  helix:  0.81 (0.26), residues: 390
  sheet:  0.11 (0.72), residues: 51
  loop : -0.87 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 168 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.010   0.001   PHE A 230 
 TYR   0.019   0.002   TYR A 183 
 ARG   0.004   0.001   ARG E 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00564 (    5)
  link_NAG-ASN         : angle       1.54657 (   15)
  hydrogen bonds       : bond        0.04605 (  320)
  hydrogen bonds       : angle       4.62466 (  893)
  SS BOND              : bond        0.00408 (    7)
  SS BOND              : angle       1.12864 (   14)
  covalent geometry    : bond        0.00293 ( 6672)
  covalent geometry    : angle       0.61254 ( 9071)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8152 (m-40) cc_final: 0.7870 (t0)
REVERT: A  123 MET cc_start: 0.7818 (mtm) cc_final: 0.7617 (mtt)
REVERT: A  165 TRP cc_start: 0.7218 (t60) cc_final: 0.6284 (t60)
REVERT: A  455 MET cc_start: 0.8488 (tmm) cc_final: 0.8203 (tmm)
REVERT: A  481 LYS cc_start: 0.7626 (mttt) cc_final: 0.7275 (mttt)
REVERT: A  489 GLU cc_start: 0.8822 (pm20) cc_final: 0.8558 (pm20)
REVERT: A  497 TYR cc_start: 0.7936 (m-80) cc_final: 0.6739 (m-80)
REVERT: A  505 HIS cc_start: 0.7594 (m90) cc_final: 0.7143 (m-70)
REVERT: A  557 MET cc_start: 0.9176 (tmm) cc_final: 0.8703 (tmm)
REVERT: E  340 GLU cc_start: 0.8009 (pt0) cc_final: 0.7442 (mm-30)
REVERT: E  392 PHE cc_start: 0.8557 (m-80) cc_final: 0.8230 (m-10)
REVERT: E  450 ASN cc_start: 0.8420 (m110) cc_final: 0.8196 (t0)
  outliers start: 7
  outliers final: 6
  residues processed: 112
  average time/residue: 0.1939
  time to fit residues: 28.8274
Evaluate side-chains
  95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain E residue  366 SER
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 47 optimal weight:    0.4980
   chunk 69 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.110715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.083029 restraints weight = 26265.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.086756 restraints weight = 10661.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.089236 restraints weight = 6157.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3399
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3399 r_free = 0.3399    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3399
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6684  Z= 0.130
  Angle     :  0.622  10.498   9100  Z= 0.307
  Chirality :  0.043   0.232    962
  Planarity :  0.004   0.036   1170
  Dihedral  :  4.660  25.863    967
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.67 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.38 (0.30), residues: 788
  helix:  1.11 (0.26), residues: 384
  sheet:  0.42 (0.72), residues: 50
  loop : -0.68 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.016   0.001   PHE A 603 
 TYR   0.019   0.002   TYR A 183 
 ARG   0.007   0.001   ARG A 161 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00549 (    5)
  link_NAG-ASN         : angle       1.49683 (   15)
  hydrogen bonds       : bond        0.04355 (  320)
  hydrogen bonds       : angle       4.45849 (  893)
  SS BOND              : bond        0.00469 (    7)
  SS BOND              : angle       1.37162 (   14)
  covalent geometry    : bond        0.00288 ( 6672)
  covalent geometry    : angle       0.61732 ( 9071)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8185 (m-40) cc_final: 0.7915 (t0)
REVERT: A  249 MET cc_start: 0.8230 (mmm) cc_final: 0.7938 (mmm)
REVERT: A  455 MET cc_start: 0.8393 (tmm) cc_final: 0.8086 (tmm)
REVERT: A  478 TRP cc_start: 0.7990 (m100) cc_final: 0.7555 (m100)
REVERT: A  481 LYS cc_start: 0.7429 (mttt) cc_final: 0.7188 (mttt)
REVERT: A  505 HIS cc_start: 0.7528 (m90) cc_final: 0.7045 (m-70)
REVERT: E  340 GLU cc_start: 0.7987 (pt0) cc_final: 0.7369 (mm-30)
REVERT: E  355 ARG cc_start: 0.8382 (ttt90) cc_final: 0.7673 (ttm-80)
REVERT: E  516 GLU cc_start: 0.8037 (tp30) cc_final: 0.7832 (tp30)
  outliers start: 13
  outliers final: 13
  residues processed: 103
  average time/residue: 0.2174
  time to fit residues: 29.1206
Evaluate side-chains
  98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  440 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 50 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.111168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.084787 restraints weight = 17178.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.087928 restraints weight = 8362.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.090013 restraints weight = 5373.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3414
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6684  Z= 0.131
  Angle     :  0.623   9.568   9100  Z= 0.309
  Chirality :  0.043   0.227    962
  Planarity :  0.005   0.054   1170
  Dihedral  :  4.515  23.525    967
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.82 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.53 (0.30), residues: 788
  helix:  1.17 (0.26), residues: 385
  sheet:  0.38 (0.73), residues: 51
  loop : -0.52 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.022   0.001   PHE A 327 
 TYR   0.019   0.001   TYR A 183 
 ARG   0.009   0.001   ARG E 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00558 (    5)
  link_NAG-ASN         : angle       1.50982 (   15)
  hydrogen bonds       : bond        0.04267 (  320)
  hydrogen bonds       : angle       4.42080 (  893)
  SS BOND              : bond        0.00355 (    7)
  SS BOND              : angle       1.45702 (   14)
  covalent geometry    : bond        0.00292 ( 6672)
  covalent geometry    : angle       0.61861 ( 9071)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8189 (m-40) cc_final: 0.7933 (t0)
REVERT: A  249 MET cc_start: 0.8190 (mmm) cc_final: 0.7838 (mmm)
REVERT: A  455 MET cc_start: 0.8307 (tmm) cc_final: 0.8050 (tmm)
REVERT: A  481 LYS cc_start: 0.7283 (mttt) cc_final: 0.7081 (mttt)
REVERT: A  505 HIS cc_start: 0.7564 (m90) cc_final: 0.7088 (m-70)
REVERT: E  340 GLU cc_start: 0.7946 (pt0) cc_final: 0.7374 (mm-30)
REVERT: E  392 PHE cc_start: 0.8290 (m-10) cc_final: 0.8039 (m-10)
REVERT: E  396 TYR cc_start: 0.7271 (m-10) cc_final: 0.6919 (m-10)
  outliers start: 17
  outliers final: 13
  residues processed: 100
  average time/residue: 0.2070
  time to fit residues: 27.4554
Evaluate side-chains
  97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  440 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 76 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 8 optimal weight:    5.9990
   chunk 44 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.111707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.086678 restraints weight = 20282.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.089431 restraints weight = 9153.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.090779 restraints weight = 5643.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3418
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3418 r_free = 0.3418    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3418
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6684  Z= 0.128
  Angle     :  0.643  11.255   9100  Z= 0.320
  Chirality :  0.044   0.235    962
  Planarity :  0.004   0.041   1170
  Dihedral  :  4.450  23.791    967
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.54 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.64 (0.30), residues: 788
  helix:  1.15 (0.26), residues: 389
  sheet:  0.27 (0.72), residues: 51
  loop : -0.30 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.015   0.001   PHE A 327 
 TYR   0.019   0.001   TYR A 183 
 ARG   0.006   0.001   ARG A 161 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00520 (    5)
  link_NAG-ASN         : angle       1.45724 (   15)
  hydrogen bonds       : bond        0.04182 (  320)
  hydrogen bonds       : angle       4.34862 (  893)
  SS BOND              : bond        0.00350 (    7)
  SS BOND              : angle       3.42247 (   14)
  covalent geometry    : bond        0.00286 ( 6672)
  covalent geometry    : angle       0.62667 ( 9071)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8228 (m-40) cc_final: 0.7935 (t0)
REVERT: A  249 MET cc_start: 0.8189 (mmm) cc_final: 0.7786 (mmm)
REVERT: A  455 MET cc_start: 0.8280 (tmm) cc_final: 0.7946 (tmm)
REVERT: A  481 LYS cc_start: 0.7290 (mttt) cc_final: 0.7008 (mttt)
REVERT: A  505 HIS cc_start: 0.7627 (m90) cc_final: 0.7160 (m-70)
REVERT: A  557 MET cc_start: 0.9087 (tmm) cc_final: 0.8627 (tmm)
REVERT: E  340 GLU cc_start: 0.8003 (pt0) cc_final: 0.7429 (mm-30)
REVERT: E  392 PHE cc_start: 0.8321 (m-10) cc_final: 0.8002 (m-10)
  outliers start: 19
  outliers final: 15
  residues processed: 106
  average time/residue: 0.2135
  time to fit residues: 30.3481
Evaluate side-chains
  103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  440 ASN
Chi-restraints excluded: chain E residue  478 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9980
   chunk 26 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 27 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 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 = 0.3779 r_free = 0.3779 target = 0.112612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.084475 restraints weight = 24410.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.088163 restraints weight = 10412.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.090587 restraints weight = 6172.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3426
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3426
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6684  Z= 0.123
  Angle     :  0.650  11.943   9100  Z= 0.323
  Chirality :  0.044   0.214    962
  Planarity :  0.004   0.045   1170
  Dihedral  :  4.353  22.754    967
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.97 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.74 (0.30), residues: 788
  helix:  1.22 (0.26), residues: 383
  sheet:  0.55 (0.72), residues: 49
  loop : -0.24 (0.35), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.017   0.001   PHE A 327 
 TYR   0.019   0.001   TYR E 421 
 ARG   0.006   0.001   ARG E 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00495 (    5)
  link_NAG-ASN         : angle       1.34518 (   15)
  hydrogen bonds       : bond        0.04076 (  320)
  hydrogen bonds       : angle       4.32790 (  893)
  SS BOND              : bond        0.00354 (    7)
  SS BOND              : angle       3.40614 (   14)
  covalent geometry    : bond        0.00275 ( 6672)
  covalent geometry    : angle       0.63527 ( 9071)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8207 (m-40) cc_final: 0.7944 (t0)
REVERT: A  249 MET cc_start: 0.8127 (mmm) cc_final: 0.7715 (mmm)
REVERT: A  455 MET cc_start: 0.8182 (tmm) cc_final: 0.7812 (tmm)
REVERT: A  481 LYS cc_start: 0.7267 (mttt) cc_final: 0.7055 (mttt)
REVERT: A  505 HIS cc_start: 0.7603 (m90) cc_final: 0.7156 (m-70)
REVERT: E  340 GLU cc_start: 0.7807 (pt0) cc_final: 0.7280 (mm-30)
REVERT: E  392 PHE cc_start: 0.8248 (m-80) cc_final: 0.7974 (m-10)
  outliers start: 15
  outliers final: 14
  residues processed: 108
  average time/residue: 0.2178
  time to fit residues: 31.7933
Evaluate side-chains
  103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain E residue  478 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0070
   chunk 77 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.113455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.087761 restraints weight = 19206.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.091876 restraints weight = 8743.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.092587 restraints weight = 4984.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3451
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3451 r_free = 0.3451    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3451 r_free = 0.3451    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3451
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6684  Z= 0.123
  Angle     :  0.659  11.621   9100  Z= 0.327
  Chirality :  0.043   0.211    962
  Planarity :  0.004   0.048   1170
  Dihedral  :  4.275  21.298    967
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.98 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.87 (0.31), residues: 788
  helix:  1.24 (0.27), residues: 384
  sheet:  0.59 (0.72), residues: 49
  loop : -0.07 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.020   0.001   PHE A 327 
 TYR   0.020   0.001   TYR E 421 
 ARG   0.007   0.001   ARG E 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00472 (    5)
  link_NAG-ASN         : angle       1.28803 (   15)
  hydrogen bonds       : bond        0.04045 (  320)
  hydrogen bonds       : angle       4.35255 (  893)
  SS BOND              : bond        0.00278 (    7)
  SS BOND              : angle       3.28537 (   14)
  covalent geometry    : bond        0.00278 ( 6672)
  covalent geometry    : angle       0.64492 ( 9071)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8219 (m-40) cc_final: 0.7937 (t0)
REVERT: A  249 MET cc_start: 0.8259 (mmm) cc_final: 0.7813 (mmm)
REVERT: A  350 ASP cc_start: 0.7515 (t0) cc_final: 0.7298 (t0)
REVERT: A  505 HIS cc_start: 0.7631 (m90) cc_final: 0.7191 (m-70)
REVERT: E  340 GLU cc_start: 0.7874 (pt0) cc_final: 0.7363 (mm-30)
REVERT: E  392 PHE cc_start: 0.8312 (m-80) cc_final: 0.7987 (m-10)
  outliers start: 18
  outliers final: 15
  residues processed: 110
  average time/residue: 0.1893
  time to fit residues: 28.2564
Evaluate side-chains
  107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain E residue  440 ASN
Chi-restraints excluded: chain E residue  478 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0040
   chunk 56 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 58 optimal weight:    0.2980
   overall best weight:    0.8598

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

Flipped N/Q/H residues before XYZ refinement:
A 472 GLN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.112000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.083784 restraints weight = 26937.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.087544 restraints weight = 10960.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.090032 restraints weight = 6368.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3417
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3417 r_free = 0.3417    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3417
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6684  Z= 0.137
  Angle     :  0.672  11.635   9100  Z= 0.332
  Chirality :  0.043   0.213    962
  Planarity :  0.004   0.038   1170
  Dihedral  :  4.281  21.565    967
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.12 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.83 (0.31), residues: 788
  helix:  1.17 (0.27), residues: 387
  sheet:  0.66 (0.72), residues: 49
  loop : -0.04 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.018   0.001   PHE A 603 
 TYR   0.020   0.001   TYR E 421 
 ARG   0.007   0.001   ARG E 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00544 (    5)
  link_NAG-ASN         : angle       1.36413 (   15)
  hydrogen bonds       : bond        0.04170 (  320)
  hydrogen bonds       : angle       4.39117 (  893)
  SS BOND              : bond        0.00412 (    7)
  SS BOND              : angle       3.27625 (   14)
  covalent geometry    : bond        0.00314 ( 6672)
  covalent geometry    : angle       0.65869 ( 9071)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8213 (m-40) cc_final: 0.7943 (t0)
REVERT: A  249 MET cc_start: 0.8163 (mmm) cc_final: 0.7720 (mmm)
REVERT: A  455 MET cc_start: 0.8104 (tmm) cc_final: 0.7793 (ttp)
REVERT: A  497 TYR cc_start: 0.7847 (m-80) cc_final: 0.6537 (m-80)
REVERT: A  505 HIS cc_start: 0.7563 (m90) cc_final: 0.7159 (m-70)
REVERT: E  340 GLU cc_start: 0.7750 (pt0) cc_final: 0.7322 (mm-30)
REVERT: E  389 ASP cc_start: 0.8777 (m-30) cc_final: 0.8574 (m-30)
REVERT: E  392 PHE cc_start: 0.8438 (m-80) cc_final: 0.8114 (m-10)
REVERT: E  469 SER cc_start: 0.8939 (t) cc_final: 0.8653 (p)
  outliers start: 18
  outliers final: 16
  residues processed: 107
  average time/residue: 0.1904
  time to fit residues: 27.2238
Evaluate side-chains
  106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain E residue  440 ASN
Chi-restraints excluded: chain E residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 45 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.110449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.082142 restraints weight = 26973.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.085858 restraints weight = 11142.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.088334 restraints weight = 6505.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3387
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6684  Z= 0.174
  Angle     :  0.718  11.709   9100  Z= 0.354
  Chirality :  0.045   0.208    962
  Planarity :  0.005   0.058   1170
  Dihedral  :  4.519  22.635    967
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.55 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.72 (0.30), residues: 788
  helix:  1.05 (0.26), residues: 388
  sheet:  0.49 (0.70), residues: 49
  loop : -0.05 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.018   0.001   PHE A 603 
 TYR   0.022   0.002   TYR E 421 
 ARG   0.004   0.001   ARG A 219 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00657 (    5)
  link_NAG-ASN         : angle       1.49102 (   15)
  hydrogen bonds       : bond        0.04469 (  320)
  hydrogen bonds       : angle       4.53696 (  893)
  SS BOND              : bond        0.00253 (    7)
  SS BOND              : angle       3.34543 (   14)
  covalent geometry    : bond        0.00400 ( 6672)
  covalent geometry    : angle       0.70493 ( 9071)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8215 (m-40) cc_final: 0.7963 (t0)
REVERT: A  152 MET cc_start: 0.8070 (tpp) cc_final: 0.7395 (tpt)
REVERT: A  222 LEU cc_start: 0.8275 (tp) cc_final: 0.7954 (tp)
REVERT: A  249 MET cc_start: 0.8127 (mmm) cc_final: 0.7679 (mmm)
REVERT: A  455 MET cc_start: 0.8103 (tmm) cc_final: 0.7769 (ttp)
REVERT: A  505 HIS cc_start: 0.7573 (m90) cc_final: 0.7158 (m-70)
REVERT: A  557 MET cc_start: 0.9075 (tmm) cc_final: 0.8609 (tmm)
REVERT: E  340 GLU cc_start: 0.7805 (pt0) cc_final: 0.7361 (mm-30)
REVERT: E  357 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7307 (tpm-80)
REVERT: E  392 PHE cc_start: 0.8457 (m-80) cc_final: 0.8162 (m-10)
  outliers start: 17
  outliers final: 15
  residues processed: 102
  average time/residue: 0.1929
  time to fit residues: 26.4909
Evaluate side-chains
  104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  357 ARG
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain E residue  440 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    0.0270
   chunk 77 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 27 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.113006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.086633 restraints weight = 17291.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.089863 restraints weight = 8388.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.091980 restraints weight = 5363.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3450
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3450 r_free = 0.3450    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3450 r_free = 0.3450    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3450
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6684  Z= 0.129
  Angle     :  0.695  11.566   9100  Z= 0.342
  Chirality :  0.043   0.210    962
  Planarity :  0.004   0.054   1170
  Dihedral  :  4.369  21.205    967
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.84 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.80 (0.31), residues: 788
  helix:  1.11 (0.27), residues: 390
  sheet:  0.39 (0.70), residues: 49
  loop :  0.02 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.017   0.001   PHE A 603 
 TYR   0.021   0.001   TYR E 421 
 ARG   0.008   0.001   ARG E 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00469 (    5)
  link_NAG-ASN         : angle       1.30727 (   15)
  hydrogen bonds       : bond        0.04154 (  320)
  hydrogen bonds       : angle       4.43347 (  893)
  SS BOND              : bond        0.00197 (    7)
  SS BOND              : angle       3.26086 (   14)
  covalent geometry    : bond        0.00292 ( 6672)
  covalent geometry    : angle       0.68213 ( 9071)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2990.97 seconds
wall clock time: 52 minutes 52.37 seconds (3172.37 seconds total)