Starting phenix.real_space_refine
on Sat May 10 16:49:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qsq_18639/05_2025/8qsq_18639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qsq_18639/05_2025/8qsq_18639.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qsq_18639/05_2025/8qsq_18639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qsq_18639/05_2025/8qsq_18639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qsq_18639/05_2025/8qsq_18639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qsq_18639/05_2025/8qsq_18639.cif"
  }
  resolution = 3.7
  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=   0.024
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    4174      2.51       5
     N    1073      2.21       5
     O    1228      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6512
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1566
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 13, 'TRANS': 181}
    Chain: "B"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 4.41, per 1000 atoms: 0.68
  Number of scatterers: 6512
  At special positions: 0
  Unit cell: (74.46, 99.28, 116.8, 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    1228      8.00
     N    1073      7.00
     C    4174      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 333 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 429 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 388 " - pdb=" SG  CYS A 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 477 " - pdb=" SG  CYS A 484 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 344 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 530 " - pdb=" SG  CYS B 542 " 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 B 801 " - " ASN B 322 "
      " NAG B 802 " - " ASN B 546 "
      " NAG B 803 " - " ASN B 432 "
      " NAG B 804 " - " ASN B  53 "
      " NAG B 805 " - " ASN B  90 "
      " NAG B 806 " - " ASN B 103 "
  Time building additional restraints: 1.51
  Conformation dependent library (CDL) restraints added in 813.8 milliseconds
  

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 7 sheets defined
      58.2% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 334 through 339
      removed outlier: 4.330A  pdb=" N   VAL A 338 " --> pdb=" O   PRO A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 363
      No H-bonds generated for 'chain 'A' and resid 361 through 363'
    Processing helix  chain 'A' and resid 364 through 369
      removed outlier: 3.896A  pdb=" N   ALA A 369 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 387
      removed outlier: 4.951A  pdb=" N   ASN A 385 " --> pdb=" O   THR A 382 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU A 387 " --> pdb=" O   LEU A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 405
      removed outlier: 3.854A  pdb=" N   SER A 405 " --> pdb=" O   ASN A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 419
    Processing helix  chain 'B' and resid 20 through 52
      removed outlier: 3.751A  pdb=" N   HIS B  34 " --> pdb=" O   ASP B  30 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP B  38 " --> pdb=" O   HIS B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 81
      removed outlier: 3.505A  pdb=" N   VAL B  59 " --> pdb=" O   THR B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 83
      No H-bonds generated for 'chain 'B' and resid 82 through 83'
    Processing helix  chain 'B' and resid 84 through 88
    Processing helix  chain 'B' and resid 90 through 102
      removed outlier: 3.539A  pdb=" N   GLN B  96 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 3.620A  pdb=" N   SER B 106 " --> pdb=" O   ASN B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 130
    Processing helix  chain 'B' and resid 146 through 155
    Processing helix  chain 'B' and resid 157 through 172
      removed outlier: 3.651A  pdb=" N   ARG B 169 " --> pdb=" O   TRP B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 194
      Proline residue:  B 178  - end of helix
      removed outlier: 3.543A  pdb=" N   GLU B 182 " --> pdb=" O   PRO B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 204
    Processing helix  chain 'B' and resid 205 through 208
    Processing helix  chain 'B' and resid 218 through 252
      removed outlier: 3.757A  pdb=" N   LEU B 222 " --> pdb=" O   SER B 218 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ILE B 223 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU B 224 " --> pdb=" O   GLY B 220 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLU B 232 " --> pdb=" O   HIS B 228 " (cutoff:3.500A)
      Proline residue:  B 235  - end of helix
    Processing helix  chain 'B' and resid 275 through 277
      No H-bonds generated for 'chain 'B' and resid 275 through 277'
    Processing helix  chain 'B' and resid 278 through 283
    Processing helix  chain 'B' and resid 293 through 300
    Processing helix  chain 'B' and resid 303 through 318
      removed outlier: 3.615A  pdb=" N   VAL B 318 " --> pdb=" O   PHE B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 331
      removed outlier: 3.568A  pdb=" N   TRP B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 385
      removed outlier: 3.526A  pdb=" N   HIS B 373 " --> pdb=" O   PHE B 369 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   HIS B 378 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 388
      No H-bonds generated for 'chain 'B' and resid 386 through 388'
    Processing helix  chain 'B' and resid 389 through 393
    Processing helix  chain 'B' and resid 399 through 413
      removed outlier: 3.803A  pdb=" N   MET B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   SER B 409 " --> pdb=" O   GLY B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 421
    Processing helix  chain 'B' and resid 431 through 446
      removed outlier: 3.651A  pdb=" N   THR B 445 " --> pdb=" O   LYS B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 465
    Processing helix  chain 'B' and resid 469 through 471
      No H-bonds generated for 'chain 'B' and resid 469 through 471'
    Processing helix  chain 'B' and resid 472 through 484
    Processing helix  chain 'B' and resid 498 through 502
    Processing helix  chain 'B' and resid 503 through 508
    Processing helix  chain 'B' and resid 513 through 533
      removed outlier: 3.702A  pdb=" N   PHE B 523 " --> pdb=" O   THR B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 542
    Processing helix  chain 'B' and resid 547 through 559
      removed outlier: 4.104A  pdb=" N   MET B 557 " --> pdb=" O   LYS B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 575
      removed outlier: 3.841A  pdb=" N   VAL B 573 " --> pdb=" O   ALA B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 581 through 588
    Processing helix  chain 'B' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355
    Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 359
      removed outlier: 7.322A  pdb=" N   CYS A 358 " --> pdb=" O   CYS A 521 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 449 through 451
    Processing sheet with id=AA4, first strand: chain 'A' and resid 470 through 471
    Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 133
    Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263
      removed outlier: 5.865A  pdb=" N   LEU B 262 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 352
      removed outlier: 6.138A  pdb=" N   ASP B 355 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)

    315 hydrogen bonds defined for protein.
    879 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: 1.84

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2073
        1.34 -     1.46: 1700
        1.46 -     1.58: 2870
        1.58 -     1.70: 0
        1.70 -     1.81: 58
  Bond restraints: 6701
  Sorted by residual:
  bond pdb=" C1  NAG B 806 "
       pdb=" O5  NAG B 806 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.07e+00
  bond pdb=" C1  NAG B 801 "
       pdb=" O5  NAG B 801 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.28e+00
  bond pdb=" C1  NAG B 805 "
       pdb=" O5  NAG B 805 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.06e+00
  bond pdb=" C1  NAG B 803 "
       pdb=" O5  NAG B 803 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C1  NAG B 802 "
       pdb=" O5  NAG B 802 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.86e+00
  ... (remaining 6696 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 8845
        1.12 -     2.24: 193
        2.24 -     3.36: 56
        3.36 -     4.48: 10
        4.48 -     5.60: 5
  Bond angle restraints: 9109
  Sorted by residual:
  angle pdb=" CA  LYS A 478 "
        pdb=" CB  LYS A 478 "
        pdb=" CG  LYS A 478 "
      ideal   model   delta    sigma   weight residual
     114.10  118.03   -3.93 2.00e+00 2.50e-01 3.85e+00
  angle pdb=" C   CYS A 477 "
        pdb=" N   LYS A 478 "
        pdb=" CA  LYS A 478 "
      ideal   model   delta    sigma   weight residual
     121.54  125.22   -3.68 1.91e+00 2.74e-01 3.72e+00
  angle pdb=" N   VAL B 573 "
        pdb=" CA  VAL B 573 "
        pdb=" C   VAL B 573 "
      ideal   model   delta    sigma   weight residual
     111.67  109.98    1.69 9.50e-01 1.11e+00 3.17e+00
  angle pdb=" CA  TYR B 385 "
        pdb=" CB  TYR B 385 "
        pdb=" CG  TYR B 385 "
      ideal   model   delta    sigma   weight residual
     113.90  117.08   -3.18 1.80e+00 3.09e-01 3.12e+00
  angle pdb=" CA  HIS A 515 "
        pdb=" C   HIS A 515 "
        pdb=" N   ALA A 516 "
      ideal   model   delta    sigma   weight residual
     118.22  116.47    1.75 1.03e+00 9.43e-01 2.89e+00
  ... (remaining 9104 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 3811
       17.29 -    34.57: 166
       34.57 -    51.86: 37
       51.86 -    69.14: 10
       69.14 -    86.43: 4
  Dihedral angle restraints: 4028
    sinusoidal: 1704
      harmonic: 2324
  Sorted by residual:
  dihedral pdb=" N   LYS B 476 "
           pdb=" CA  LYS B 476 "
           pdb=" CB  LYS B 476 "
           pdb=" CG  LYS B 476 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.49   59.49     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   HIS B 401 "
           pdb=" CA  HIS B 401 "
           pdb=" CB  HIS B 401 "
           pdb=" CG  HIS B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -128.43  -51.57     3      1.50e+01 4.44e-03 9.03e+00
  dihedral pdb=" N   GLU B  56 "
           pdb=" CA  GLU B  56 "
           pdb=" CB  GLU B  56 "
           pdb=" CG  GLU B  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -131.28  -48.72     3      1.50e+01 4.44e-03 8.68e+00
  ... (remaining 4025 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 879
       0.071 -    0.142: 83
       0.142 -    0.214: 1
       0.214 -    0.285: 1
       0.285 -    0.356: 1
  Chirality restraints: 965
  Sorted by residual:
  chirality pdb=" C1  NAG B 806 "
            pdb=" ND2 ASN B 103 "
            pdb=" C2  NAG B 806 "
            pdb=" O5  NAG B 806 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.76    0.36 2.00e-01 2.50e+01 3.17e+00
  chirality pdb=" C1  NAG B 801 "
            pdb=" ND2 ASN B 322 "
            pdb=" C2  NAG B 801 "
            pdb=" O5  NAG B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" C1  NAG B 805 "
            pdb=" ND2 ASN B  90 "
            pdb=" C2  NAG B 805 "
            pdb=" O5  NAG B 805 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.61    0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 962 not shown)

  Planarity restraints: 1177
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 103 "   -0.037 2.00e-02 2.50e+03   4.04e-02 2.05e+01
        pdb=" CG  ASN B 103 "    0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 103 "    0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 103 "    0.065 2.00e-02 2.50e+03
        pdb=" C1  NAG B 806 "   -0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 432 "   -0.026 2.00e-02 2.50e+03   2.75e-02 9.44e+00
        pdb=" CG  ASN B 432 "    0.011 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 432 "    0.006 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 432 "    0.043 2.00e-02 2.50e+03
        pdb=" C1  NAG B 803 "   -0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 322 "    0.016 2.00e-02 2.50e+03   1.77e-02 3.91e+00
        pdb=" CG  ASN B 322 "   -0.006 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 322 "   -0.002 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 322 "   -0.029 2.00e-02 2.50e+03
        pdb=" C1  NAG B 801 "    0.021 2.00e-02 2.50e+03
  ... (remaining 1174 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1662
        2.79 -     3.32: 6121
        3.32 -     3.85: 11106
        3.85 -     4.37: 13721
        4.37 -     4.90: 22537
  Nonbonded interactions: 55147
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 607 "
            pdb=" OD1 ASP B 609 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" NZ  LYS B 288 "
            pdb=" OD2 ASP B 431 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O   ASP B 499 "
            pdb=" OG  SER B 502 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OG1 THR B 276 "
            pdb=" OG1 THR B 445 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" NZ  LYS B  31 "
            pdb=" OE2 GLU B  35 "
     model   vdw
     2.330 3.120
  ... (remaining 55142 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.100
  Process input model:                     18.090
  Find NCS groups from input model:        0.050
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
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   0.232   6714  Z= 0.217
  Angle     :  0.521  16.915   9141  Z= 0.245
  Chirality :  0.043   0.356    965
  Planarity :  0.003   0.031   1171
  Dihedral  : 10.949  86.426   2515
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  4.17 %
    Favored  : 94.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.28), residues: 787
  helix: -1.37 (0.21), residues: 390
  sheet:  0.15 (0.74), residues: 49
  loop : -0.35 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 478 
 HIS   0.003   0.001   HIS B 241 
 PHE   0.006   0.001   PHE B 523 
 TYR   0.015   0.001   TYR B 385 
 ARG   0.002   0.000   ARG B 245 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.11917 (    6)
  link_NAG-ASN         : angle       5.44079 (   18)
  hydrogen bonds       : bond        0.22606 (  315)
  hydrogen bonds       : angle       7.28511 (  879)
  SS BOND              : bond        0.00224 (    7)
  SS BOND              : angle       0.55736 (   14)
  covalent geometry    : bond        0.00238 ( 6701)
  covalent geometry    : angle       0.46197 ( 9109)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  367 ASN cc_start: 0.8572 (m-40) cc_final: 0.8165 (t0)
REVERT: A  415 ILE cc_start: 0.8974 (mm) cc_final: 0.8569 (pt)
REVERT: B   56 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8579 (pm20)
REVERT: B  213 ASP cc_start: 0.9163 (m-30) cc_final: 0.8412 (p0)
REVERT: B  322 ASN cc_start: 0.4723 (OUTLIER) cc_final: 0.4312 (p0)
REVERT: B  323 MET cc_start: 0.6861 (mmp) cc_final: 0.6469 (mmp)
REVERT: B  455 MET cc_start: 0.5113 (tmt) cc_final: 0.3262 (ttp)
REVERT: B  474 MET cc_start: -0.0441 (mmm) cc_final: -0.2701 (mmp)
REVERT: B  572 ASN cc_start: 0.7642 (m-40) cc_final: 0.7303 (t0)
  outliers start: 8
  outliers final: 1
  residues processed: 91
  average time/residue: 0.2198
  time to fit residues: 25.8885
Evaluate side-chains
  42 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 GLU
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain B residue  401 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 20 optimal weight:   20.0000
   chunk 39 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 37 optimal weight:   30.0000
   chunk 45 optimal weight:    8.9990
   chunk 70 optimal weight:    0.0270
   overall best weight:    6.6046

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

Flipped N/Q/H residues before XYZ refinement:
A 483 ASN
** B  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 ASN
B 210 ASN
B 340 GLN
B 552 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.048322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.039682 restraints weight = 95996.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.040568 restraints weight = 57784.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.041196 restraints weight = 39808.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   6714  Z= 0.234
  Angle     :  0.713   7.502   9141  Z= 0.379
  Chirality :  0.045   0.198    965
  Planarity :  0.006   0.057   1171
  Dihedral  :  5.935  58.211    991
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 10.36 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.00 (0.29), residues: 787
  helix:  0.38 (0.24), residues: 390
  sheet:  0.11 (0.74), residues: 49
  loop : -0.30 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 328 
 HIS   0.008   0.002   HIS A 501 
 PHE   0.018   0.002   PHE A 368 
 TYR   0.029   0.002   TYR B 385 
 ARG   0.006   0.001   ARG A 354 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00474 (    6)
  link_NAG-ASN         : angle       1.78832 (   18)
  hydrogen bonds       : bond        0.04896 (  315)
  hydrogen bonds       : angle       5.21342 (  879)
  SS BOND              : bond        0.00448 (    7)
  SS BOND              : angle       0.78316 (   14)
  covalent geometry    : bond        0.00482 ( 6701)
  covalent geometry    : angle       0.70877 ( 9109)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.710 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  123 MET cc_start: 0.4795 (mtp) cc_final: 0.4594 (ptm)
REVERT: B  455 MET cc_start: 0.4488 (tmt) cc_final: 0.3255 (ttp)
REVERT: B  572 ASN cc_start: 0.8589 (m-40) cc_final: 0.8087 (t0)
  outliers start: 13
  outliers final: 8
  residues processed: 50
  average time/residue: 0.1735
  time to fit residues: 12.3872
Evaluate side-chains
  38 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  341 LYS
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  522 GLN
Chi-restraints excluded: chain B residue  534 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 49 optimal weight:   50.0000
   chunk 77 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 483 ASN
B 472 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.049090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.041038 restraints weight = 86611.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.041927 restraints weight = 51432.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.042507 restraints weight = 34488.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.4499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6714  Z= 0.129
  Angle     :  0.549   8.006   9141  Z= 0.286
  Chirality :  0.041   0.163    965
  Planarity :  0.004   0.031   1171
  Dihedral  :  4.436  23.073    984
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.22 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.29), residues: 787
  helix:  0.83 (0.26), residues: 393
  sheet:  0.48 (0.75), residues: 51
  loop : -0.18 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 328 
 HIS   0.007   0.001   HIS A 501 
 PHE   0.015   0.001   PHE B 315 
 TYR   0.016   0.001   TYR B  50 
 ARG   0.003   0.000   ARG A 494 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00207 (    6)
  link_NAG-ASN         : angle       1.67767 (   18)
  hydrogen bonds       : bond        0.04038 (  315)
  hydrogen bonds       : angle       4.73173 (  879)
  SS BOND              : bond        0.00288 (    7)
  SS BOND              : angle       0.67421 (   14)
  covalent geometry    : bond        0.00265 ( 6701)
  covalent geometry    : angle       0.54467 ( 9109)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 29
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   82 MET cc_start: 0.8435 (mpp) cc_final: 0.7874 (ppp)
REVERT: B  455 MET cc_start: 0.3856 (tmt) cc_final: 0.3372 (ttp)
REVERT: B  494 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7980 (p0)
REVERT: B  557 MET cc_start: 0.6009 (tmm) cc_final: 0.5759 (tmm)
REVERT: B  572 ASN cc_start: 0.8632 (m-40) cc_final: 0.8051 (t0)
  outliers start: 12
  outliers final: 6
  residues processed: 41
  average time/residue: 0.1528
  time to fit residues: 9.7183
Evaluate side-chains
  35 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain B residue   60 GLN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  494 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 52 optimal weight:    0.5980
   chunk 58 optimal weight:   50.0000
   chunk 59 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   overall best weight:    4.7188

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

Flipped N/Q/H residues before XYZ refinement:
B  96 GLN
B 305 GLN
** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.047154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.039179 restraints weight = 89110.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.040015 restraints weight = 52998.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.040572 restraints weight = 35625.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.5616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6714  Z= 0.170
  Angle     :  0.598   6.543   9141  Z= 0.312
  Chirality :  0.042   0.211    965
  Planarity :  0.004   0.032   1171
  Dihedral  :  4.915  29.498    984
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  9.93 %
    Favored  : 87.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.28 (0.29), residues: 787
  helix:  0.58 (0.25), residues: 402
  sheet:  0.61 (0.80), residues: 48
  loop : -0.22 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 478 
 HIS   0.007   0.002   HIS B 535 
 PHE   0.017   0.002   PHE B 315 
 TYR   0.017   0.002   TYR B 385 
 ARG   0.007   0.001   ARG A 494 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    6)
  link_NAG-ASN         : angle       1.88819 (   18)
  hydrogen bonds       : bond        0.04123 (  315)
  hydrogen bonds       : angle       4.95171 (  879)
  SS BOND              : bond        0.00361 (    7)
  SS BOND              : angle       0.78146 (   14)
  covalent geometry    : bond        0.00352 ( 6701)
  covalent geometry    : angle       0.59232 ( 9109)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 29
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
REVERT: B   82 MET cc_start: 0.8343 (mpp) cc_final: 0.7882 (ppp)
REVERT: B  323 MET cc_start: 0.7809 (mmt) cc_final: 0.7529 (mmt)
REVERT: B  455 MET cc_start: 0.4063 (tmt) cc_final: 0.3596 (ttp)
REVERT: B  474 MET cc_start: -0.2265 (mmp) cc_final: -0.2745 (mmp)
REVERT: B  485 VAL cc_start: 0.6592 (OUTLIER) cc_final: 0.5940 (t)
REVERT: B  494 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8105 (p0)
REVERT: B  572 ASN cc_start: 0.8742 (m-40) cc_final: 0.8325 (t0)
  outliers start: 17
  outliers final: 10
  residues processed: 45
  average time/residue: 0.1409
  time to fit residues: 10.0950
Evaluate side-chains
  40 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  494 ASP
Chi-restraints excluded: chain B residue  504 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   chunk 63 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:   40.0000
   chunk 8 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   overall best weight:    7.7990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.045274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.037473 restraints weight = 91666.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.038311 restraints weight = 53140.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.038880 restraints weight = 35271.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.7276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6714  Z= 0.262
  Angle     :  0.768   8.018   9141  Z= 0.403
  Chirality :  0.047   0.296    965
  Planarity :  0.006   0.041   1171
  Dihedral  :  5.950  30.861    984
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 26.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 10.50 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.28), residues: 787
  helix: -0.22 (0.24), residues: 402
  sheet:  0.63 (0.72), residues: 45
  loop : -0.78 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 275 
 HIS   0.010   0.002   HIS B 535 
 PHE   0.023   0.003   PHE B 315 
 TYR   0.028   0.002   TYR B  50 
 ARG   0.008   0.001   ARG A 494 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00364 (    6)
  link_NAG-ASN         : angle       2.55355 (   18)
  hydrogen bonds       : bond        0.04919 (  315)
  hydrogen bonds       : angle       5.63474 (  879)
  SS BOND              : bond        0.00548 (    7)
  SS BOND              : angle       1.17234 (   14)
  covalent geometry    : bond        0.00549 ( 6701)
  covalent geometry    : angle       0.75997 ( 9109)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 27
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: B   82 MET cc_start: 0.8383 (mpp) cc_final: 0.7726 (ppp)
REVERT: B  332 MET cc_start: 0.8029 (tpp) cc_final: 0.7600 (tpt)
REVERT: B  339 VAL cc_start: 0.2970 (OUTLIER) cc_final: 0.2378 (m)
REVERT: B  462 MET cc_start: 0.6246 (mmp) cc_final: 0.5844 (mmp)
REVERT: B  485 VAL cc_start: 0.6683 (OUTLIER) cc_final: 0.5777 (t)
REVERT: B  572 ASN cc_start: 0.8991 (m-40) cc_final: 0.8595 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 44
  average time/residue: 0.1501
  time to fit residues: 10.1009
Evaluate side-chains
  37 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 24
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  440 LEU
Chi-restraints excluded: chain B residue  485 VAL
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  534 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:   20.0000
   chunk 52 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 63 optimal weight:    2.9990
   chunk 26 optimal weight:   20.0000
   chunk 51 optimal weight:   20.0000
   chunk 10 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 194 ASN
** B 472 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 = 0.3887 r_free = 0.3887 target = 0.045781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.038046 restraints weight = 90498.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.038879 restraints weight = 52370.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.039424 restraints weight = 34543.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.7413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6714  Z= 0.188
  Angle     :  0.655   9.275   9141  Z= 0.342
  Chirality :  0.044   0.269    965
  Planarity :  0.005   0.040   1171
  Dihedral  :  5.293  23.701    984
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 21.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 11.22 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.41 (0.29), residues: 787
  helix:  0.08 (0.25), residues: 397
  sheet:  0.96 (0.74), residues: 45
  loop : -0.75 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 478 
 HIS   0.008   0.002   HIS A 501 
 PHE   0.013   0.002   PHE A 374 
 TYR   0.023   0.002   TYR B 237 
 ARG   0.006   0.001   ARG A 494 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00245 (    6)
  link_NAG-ASN         : angle       2.36613 (   18)
  hydrogen bonds       : bond        0.04404 (  315)
  hydrogen bonds       : angle       5.40102 (  879)
  SS BOND              : bond        0.00373 (    7)
  SS BOND              : angle       0.94257 (   14)
  covalent geometry    : bond        0.00397 ( 6701)
  covalent geometry    : angle       0.64701 ( 9109)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 25
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
REVERT: B   82 MET cc_start: 0.8372 (mpp) cc_final: 0.8032 (ppp)
REVERT: B  271 TRP cc_start: 0.0368 (OUTLIER) cc_final: -0.1667 (m-90)
REVERT: B  323 MET cc_start: 0.7995 (mmt) cc_final: 0.7460 (mmt)
REVERT: B  339 VAL cc_start: 0.2905 (OUTLIER) cc_final: 0.2385 (m)
REVERT: B  462 MET cc_start: 0.5842 (mmp) cc_final: 0.5476 (mmp)
REVERT: B  512 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7374 (t80)
REVERT: B  572 ASN cc_start: 0.9035 (m-40) cc_final: 0.8609 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 42
  average time/residue: 0.1513
  time to fit residues: 9.7651
Evaluate side-chains
  38 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 23
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  271 TRP
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  512 PHE
Chi-restraints excluded: chain B residue  534 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 56 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 71 optimal weight:    7.9990
   chunk 34 optimal weight:   20.0000
   chunk 62 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   chunk 66 optimal weight:    0.7980
   chunk 43 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 241 HIS
B 277 ASN
** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.045968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.038353 restraints weight = 90680.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.039201 restraints weight = 52044.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.039748 restraints weight = 34171.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.7655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6714  Z= 0.163
  Angle     :  0.630   9.405   9141  Z= 0.326
  Chirality :  0.043   0.239    965
  Planarity :  0.004   0.037   1171
  Dihedral  :  4.951  19.349    984
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 19.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 11.65 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.30 (0.30), residues: 787
  helix:  0.12 (0.25), residues: 408
  sheet:  1.11 (0.75), residues: 45
  loop : -0.65 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 478 
 HIS   0.007   0.002   HIS A 501 
 PHE   0.021   0.002   PHE B 315 
 TYR   0.025   0.002   TYR B 237 
 ARG   0.005   0.001   ARG A 494 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00151 (    6)
  link_NAG-ASN         : angle       2.09375 (   18)
  hydrogen bonds       : bond        0.04207 (  315)
  hydrogen bonds       : angle       5.29150 (  879)
  SS BOND              : bond        0.00325 (    7)
  SS BOND              : angle       0.77507 (   14)
  covalent geometry    : bond        0.00341 ( 6701)
  covalent geometry    : angle       0.62332 ( 9109)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 23
  time to evaluate  : 0.765 
Fit side-chains
REVERT: B   82 MET cc_start: 0.8193 (mpp) cc_final: 0.7967 (ppp)
REVERT: B  474 MET cc_start: -0.3091 (mmp) cc_final: -0.3414 (mmp)
REVERT: B  480 MET cc_start: 0.6987 (ptt) cc_final: 0.5948 (ttt)
REVERT: B  494 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8185 (p0)
REVERT: B  512 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7277 (t80)
REVERT: B  572 ASN cc_start: 0.9008 (m-40) cc_final: 0.8661 (t0)
  outliers start: 18
  outliers final: 10
  residues processed: 39
  average time/residue: 0.1424
  time to fit residues: 8.8558
Evaluate side-chains
  35 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 23
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  494 ASP
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  512 PHE
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 59 optimal weight:   20.0000
   chunk 14 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 2 optimal weight:    8.9990
   chunk 51 optimal weight:   50.0000
   chunk 70 optimal weight:    9.9990
   chunk 47 optimal weight:   10.0000
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 586 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.044827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.037019 restraints weight = 91690.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.037836 restraints weight = 53556.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.038366 restraints weight = 35672.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.8373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   6714  Z= 0.231
  Angle     :  0.749  16.581   9141  Z= 0.384
  Chirality :  0.046   0.323    965
  Planarity :  0.005   0.038   1171
  Dihedral  :  5.678  26.464    984
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 25.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.23 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.67 (0.29), residues: 787
  helix: -0.19 (0.24), residues: 407
  sheet:  0.60 (0.71), residues: 45
  loop : -0.76 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 275 
 HIS   0.009   0.002   HIS B 535 
 PHE   0.023   0.002   PHE B 315 
 TYR   0.018   0.002   TYR B 237 
 ARG   0.006   0.001   ARG A 494 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00199 (    6)
  link_NAG-ASN         : angle       2.86523 (   18)
  hydrogen bonds       : bond        0.04696 (  315)
  hydrogen bonds       : angle       5.57980 (  879)
  SS BOND              : bond        0.00475 (    7)
  SS BOND              : angle       0.95877 (   14)
  covalent geometry    : bond        0.00488 ( 6701)
  covalent geometry    : angle       0.73811 ( 9109)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 24
  time to evaluate  : 0.777 
Fit side-chains
REVERT: B   82 MET cc_start: 0.8307 (mpp) cc_final: 0.7975 (ppp)
REVERT: B  222 LEU cc_start: 0.8651 (tp) cc_final: 0.8389 (mt)
REVERT: B  376 MET cc_start: 0.7918 (ttm) cc_final: 0.7421 (ptm)
REVERT: B  480 MET cc_start: 0.6759 (ptt) cc_final: 0.5978 (ttm)
REVERT: B  572 ASN cc_start: 0.9035 (m-40) cc_final: 0.8602 (t0)
  outliers start: 15
  outliers final: 11
  residues processed: 38
  average time/residue: 0.1556
  time to fit residues: 9.1317
Evaluate side-chains
  35 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 24
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  534 LYS
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  34 HIS
B 472 GLN
** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.045747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.038192 restraints weight = 91355.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.039026 restraints weight = 53137.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.039563 restraints weight = 35149.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.8301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6714  Z= 0.165
  Angle     :  0.647  11.806   9141  Z= 0.337
  Chirality :  0.044   0.281    965
  Planarity :  0.004   0.036   1171
  Dihedral  :  5.387  27.678    984
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 20.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.66 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.30), residues: 787
  helix: -0.05 (0.25), residues: 407
  sheet:  0.94 (0.73), residues: 45
  loop : -0.70 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 275 
 HIS   0.007   0.002   HIS B 535 
 PHE   0.018   0.002   PHE B 315 
 TYR   0.018   0.002   TYR B 454 
 ARG   0.005   0.001   ARG A 494 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00134 (    6)
  link_NAG-ASN         : angle       2.40179 (   18)
  hydrogen bonds       : bond        0.04425 (  315)
  hydrogen bonds       : angle       5.45651 (  879)
  SS BOND              : bond        0.00306 (    7)
  SS BOND              : angle       0.80468 (   14)
  covalent geometry    : bond        0.00346 ( 6701)
  covalent geometry    : angle       0.63853 ( 9109)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 25
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
REVERT: B  222 LEU cc_start: 0.8583 (tp) cc_final: 0.8245 (mt)
REVERT: B  271 TRP cc_start: 0.0937 (OUTLIER) cc_final: -0.1527 (m-90)
REVERT: B  332 MET cc_start: 0.8171 (tpp) cc_final: 0.7935 (tpp)
REVERT: B  376 MET cc_start: 0.7840 (ttm) cc_final: 0.7567 (ptm)
REVERT: B  474 MET cc_start: -0.2567 (mmp) cc_final: -0.2833 (mmp)
REVERT: B  572 ASN cc_start: 0.9016 (m-40) cc_final: 0.8691 (t0)
  outliers start: 15
  outliers final: 13
  residues processed: 39
  average time/residue: 0.1671
  time to fit residues: 9.6478
Evaluate side-chains
  38 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 24
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  271 TRP
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  453 THR
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  534 LYS
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 69 optimal weight:    9.9990
   chunk 58 optimal weight:   20.0000
   chunk 16 optimal weight:   10.0000
   chunk 49 optimal weight:    8.9990
   chunk 42 optimal weight:   20.0000
   chunk 63 optimal weight:    0.0470
   chunk 44 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    7.0086

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

Flipped N/Q/H residues before XYZ refinement:
B 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.044735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.037076 restraints weight = 92637.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.037872 restraints weight = 54758.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.038405 restraints weight = 36541.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.8831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6714  Z= 0.231
  Angle     :  0.744  12.708   9141  Z= 0.387
  Chirality :  0.047   0.324    965
  Planarity :  0.005   0.037   1171
  Dihedral  :  6.089  37.236    984
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 25.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 12.95 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.78 (0.29), residues: 787
  helix: -0.26 (0.24), residues: 407
  sheet:  0.56 (0.71), residues: 45
  loop : -0.84 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 275 
 HIS   0.009   0.002   HIS B 535 
 PHE   0.018   0.002   PHE B 315 
 TYR   0.029   0.002   TYR B 454 
 ARG   0.007   0.001   ARG A 494 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00178 (    6)
  link_NAG-ASN         : angle       2.88994 (   18)
  hydrogen bonds       : bond        0.04788 (  315)
  hydrogen bonds       : angle       5.69025 (  879)
  SS BOND              : bond        0.00459 (    7)
  SS BOND              : angle       0.93257 (   14)
  covalent geometry    : bond        0.00484 ( 6701)
  covalent geometry    : angle       0.73280 ( 9109)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 24
  time to evaluate  : 0.818 
Fit side-chains
REVERT: B  222 LEU cc_start: 0.8621 (tp) cc_final: 0.8287 (mt)
REVERT: B  271 TRP cc_start: 0.2120 (OUTLIER) cc_final: -0.0576 (m-90)
REVERT: B  332 MET cc_start: 0.8255 (tpp) cc_final: 0.7960 (tpp)
REVERT: B  474 MET cc_start: -0.1652 (mmp) cc_final: -0.1989 (mmp)
REVERT: B  572 ASN cc_start: 0.9029 (m-40) cc_final: 0.8629 (t0)
  outliers start: 14
  outliers final: 12
  residues processed: 37
  average time/residue: 0.1713
  time to fit residues: 9.5265
Evaluate side-chains
  37 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 24
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 PHE
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  386 ASP
Chi-restraints excluded: chain A residue  402 ASN
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  271 TRP
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  453 THR
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  534 LYS
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    9.9990
   chunk 46 optimal weight:   40.0000
   chunk 6 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 14 optimal weight:   30.0000
   chunk 32 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 72 optimal weight:   20.0000
   chunk 33 optimal weight:    9.9990
   chunk 31 optimal weight:    8.9990
   overall best weight:    4.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.045523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.037996 restraints weight = 92467.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.038810 restraints weight = 54558.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.039330 restraints weight = 36401.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.8766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6714  Z= 0.169
  Angle     :  0.665  11.383   9141  Z= 0.345
  Chirality :  0.045   0.299    965
  Planarity :  0.005   0.034   1171
  Dihedral  :  5.828  38.477    984
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 21.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.95 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.60 (0.30), residues: 787
  helix: -0.10 (0.25), residues: 408
  sheet:  0.80 (0.72), residues: 45
  loop : -0.82 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 275 
 HIS   0.007   0.002   HIS B 535 
 PHE   0.013   0.002   PHE B  40 
 TYR   0.024   0.002   TYR B 454 
 ARG   0.005   0.001   ARG A 494 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00139 (    6)
  link_NAG-ASN         : angle       2.56039 (   18)
  hydrogen bonds       : bond        0.04404 (  315)
  hydrogen bonds       : angle       5.59447 (  879)
  SS BOND              : bond        0.00319 (    7)
  SS BOND              : angle       0.82586 (   14)
  covalent geometry    : bond        0.00355 ( 6701)
  covalent geometry    : angle       0.65573 ( 9109)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2769.91 seconds
wall clock time: 49 minutes 13.08 seconds (2953.08 seconds total)