Starting phenix.real_space_refine
on Fri Aug 22 17:51:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qsq_18639/08_2025/8qsq_18639.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qsq_18639/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qsq_18639/08_2025/8qsq_18639.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qsq_18639/08_2025/8qsq_18639.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qsq_18639/08_2025/8qsq_18639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qsq_18639/08_2025/8qsq_18639.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.69, per 1000 atoms: 0.26
  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: 0.55
  Conformation dependent library (CDL) restraints added in 372.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.28
  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: 1.05

  Time building geometry restraints manager: 0.75 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:             1.380
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.890
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.740
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG B 245 
 TYR   0.015   0.001   TYR B 385 
 PHE   0.006   0.001   PHE B 523 
 TRP   0.009   0.001   TRP B 478 
 HIS   0.003   0.001   HIS B 241 

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

*********************** 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  : 0.276 
Fit side-chains
   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: 0.8570 (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: 0.4387 (p0)
REVERT: B  455 MET cc_start: 0.5113 (tmt) cc_final: 0.2974 (tmm)
REVERT: B  474 MET cc_start: -0.0441 (mmm) cc_final: -0.2674 (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: 0.1067
  time to fit residues: 12.5637
Evaluate side-chains
  43 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
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 49 optimal weight:   30.0000
   chunk 53 optimal weight:   30.0000
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    8.9990
   overall best weight:    8.9990

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

Flipped N/Q/H residues before XYZ refinement:
B  76 GLN
B 139 GLN
B 149 ASN
B 210 ASN
B 305 GLN
** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 472 GLN
B 552 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.046764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.037897 restraints weight = 99162.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.038792 restraints weight = 58867.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.039366 restraints weight = 40350.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.039754 restraints weight = 30802.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.040004 restraints weight = 25418.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.5039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   6714  Z= 0.305
  Angle     :  0.828   8.370   9141  Z= 0.441
  Chirality :  0.048   0.277    965
  Planarity :  0.007   0.080   1171
  Dihedral  :  6.665  56.900    991
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 24.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.08 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.28), residues: 787
  helix: -0.05 (0.24), residues: 393
  sheet: -0.26 (0.70), residues: 51
  loop : -0.47 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 494 
 TYR   0.032   0.003   TYR B 385 
 PHE   0.030   0.003   PHE B 315 
 TRP   0.024   0.002   TRP A 433 
 HIS   0.011   0.003   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00628 ( 6701)
  covalent geometry    : angle       0.82256 ( 9109)
  SS BOND              : bond        0.00585 (    7)
  SS BOND              : angle       1.03091 (   14)
  hydrogen bonds       : bond        0.05503 (  315)
  hydrogen bonds       : angle       5.63209 (  879)
  link_NAG-ASN         : bond        0.00962 (    6)
  link_NAG-ASN         : angle       2.25882 (   18)

*********************** 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
  50 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 36
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 GLN cc_start: 0.9361 (tt0) cc_final: 0.9105 (tp-100)
REVERT: B  123 MET cc_start: 0.4654 (mtp) cc_final: 0.4415 (ptm)
REVERT: B  455 MET cc_start: 0.4671 (tmt) cc_final: 0.3408 (ttp)
REVERT: B  572 ASN cc_start: 0.8975 (m-40) cc_final: 0.8540 (t0)
  outliers start: 14
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0830
  time to fit residues: 5.8835
Evaluate side-chains
  39 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  469 ILE
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 71 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 29 optimal weight:   20.0000
   chunk 76 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0770
   chunk 23 optimal weight:    6.9990
   overall best weight:    1.9342

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

Flipped N/Q/H residues before XYZ refinement:
B 305 GLN
B 340 GLN
B 472 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.048651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.040715 restraints weight = 86550.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.041591 restraints weight = 51815.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.042172 restraints weight = 34892.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.042527 restraints weight = 25971.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.042749 restraints weight = 21111.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6714  Z= 0.122
  Angle     :  0.552   7.828   9141  Z= 0.287
  Chirality :  0.041   0.170    965
  Planarity :  0.004   0.030   1171
  Dihedral  :  4.637  23.582    984
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 10.50 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.29), residues: 787
  helix:  0.74 (0.25), residues: 391
  sheet:  0.45 (0.78), residues: 49
  loop : -0.33 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 494 
 TYR   0.015   0.001   TYR B 385 
 PHE   0.013   0.001   PHE B 523 
 TRP   0.016   0.001   TRP B 478 
 HIS   0.008   0.001   HIS A 501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6701)
  covalent geometry    : angle       0.54684 ( 9109)
  SS BOND              : bond        0.00259 (    7)
  SS BOND              : angle       0.73447 (   14)
  hydrogen bonds       : bond        0.04134 (  315)
  hydrogen bonds       : angle       4.87411 (  879)
  link_NAG-ASN         : bond        0.00145 (    6)
  link_NAG-ASN         : angle       1.80027 (   18)

*********************** 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
  43 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 31
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: B   82 MET cc_start: 0.8479 (mpp) cc_final: 0.7776 (ppp)
REVERT: B  222 LEU cc_start: 0.8812 (tp) cc_final: 0.8444 (mt)
REVERT: B  270 MET cc_start: 0.0418 (mmm) cc_final: -0.0179 (mmm)
REVERT: B  455 MET cc_start: 0.5122 (tmt) cc_final: 0.4345 (ttp)
REVERT: B  474 MET cc_start: -0.3013 (mmp) cc_final: -0.3255 (mmp)
REVERT: B  494 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7947 (p0)
REVERT: B  572 ASN cc_start: 0.8804 (m-40) cc_final: 0.8335 (t0)
  outliers start: 12
  outliers final: 5
  residues processed: 43
  average time/residue: 0.0729
  time to fit residues: 4.7132
Evaluate side-chains
  35 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 29
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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  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 40 optimal weight:    0.0470
   chunk 35 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 42 optimal weight:   40.0000
   chunk 11 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 56 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   overall best weight:    4.4086

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.047056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.039122 restraints weight = 90002.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.039967 restraints weight = 53501.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.040513 restraints weight = 35878.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.040863 restraints weight = 26646.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.041096 restraints weight = 21627.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.5732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6714  Z= 0.163
  Angle     :  0.590   5.676   9141  Z= 0.309
  Chirality :  0.042   0.197    965
  Planarity :  0.004   0.032   1171
  Dihedral  :  4.868  27.682    984
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.30), residues: 787
  helix:  0.66 (0.25), residues: 396
  sheet:  1.27 (0.78), residues: 43
  loop : -0.36 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 494 
 TYR   0.017   0.002   TYR B 385 
 PHE   0.016   0.002   PHE B 315 
 TRP   0.015   0.002   TRP B 478 
 HIS   0.007   0.002   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6701)
  covalent geometry    : angle       0.58547 ( 9109)
  SS BOND              : bond        0.00366 (    7)
  SS BOND              : angle       0.83224 (   14)
  hydrogen bonds       : bond        0.04150 (  315)
  hydrogen bonds       : angle       5.00563 (  879)
  link_NAG-ASN         : bond        0.00218 (    6)
  link_NAG-ASN         : angle       1.73255 (   18)

*********************** 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
  42 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 28
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: B   82 MET cc_start: 0.8276 (mpp) cc_final: 0.7786 (ppp)
REVERT: B  455 MET cc_start: 0.4890 (tmt) cc_final: 0.4555 (ttp)
REVERT: B  462 MET cc_start: 0.5605 (mmp) cc_final: 0.5138 (mmp)
REVERT: B  474 MET cc_start: -0.1350 (mmp) cc_final: -0.1588 (mmp)
REVERT: B  485 VAL cc_start: 0.6409 (OUTLIER) cc_final: 0.5532 (t)
REVERT: B  494 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7912 (p0)
REVERT: B  572 ASN cc_start: 0.8696 (m-40) cc_final: 0.8300 (t0)
  outliers start: 14
  outliers final: 10
  residues processed: 42
  average time/residue: 0.0551
  time to fit residues: 3.7042
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  : 0.297 
-------------------------------------------------------------------------------
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  581 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 30 optimal weight:   20.0000
   chunk 43 optimal weight:    0.2980
   chunk 35 optimal weight:    8.9990
   chunk 67 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    2.8586

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

Flipped N/Q/H residues before XYZ refinement:
B 290 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.047034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.038088 restraints weight = 102612.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.039033 restraints weight = 59767.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.039663 restraints weight = 40204.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.040089 restraints weight = 30165.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.040366 restraints weight = 24500.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.5855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6714  Z= 0.122
  Angle     :  0.538  10.201   9141  Z= 0.278
  Chirality :  0.041   0.181    965
  Planarity :  0.004   0.038   1171
  Dihedral  :  4.393  20.228    984
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 10.94 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.30), residues: 787
  helix:  0.85 (0.25), residues: 396
  sheet:  1.42 (0.78), residues: 43
  loop : -0.39 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 494 
 TYR   0.016   0.001   TYR B  50 
 PHE   0.011   0.001   PHE B 523 
 TRP   0.013   0.001   TRP B 478 
 HIS   0.006   0.001   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6701)
  covalent geometry    : angle       0.53391 ( 9109)
  SS BOND              : bond        0.00255 (    7)
  SS BOND              : angle       0.72003 (   14)
  hydrogen bonds       : bond        0.03735 (  315)
  hydrogen bonds       : angle       4.83085 (  879)
  link_NAG-ASN         : bond        0.00124 (    6)
  link_NAG-ASN         : angle       1.58543 (   18)

*********************** 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
  42 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 29
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: B  270 MET cc_start: 0.0084 (mmm) cc_final: -0.2354 (mmm)
REVERT: B  271 TRP cc_start: -0.0120 (OUTLIER) cc_final: -0.1917 (m-90)
REVERT: B  455 MET cc_start: 0.4741 (tmt) cc_final: 0.4451 (ttp)
REVERT: B  474 MET cc_start: -0.1198 (mmp) cc_final: -0.1807 (mmp)
REVERT: B  485 VAL cc_start: 0.6053 (OUTLIER) cc_final: 0.5295 (t)
REVERT: B  494 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8154 (p0)
REVERT: B  572 ASN cc_start: 0.8843 (m-40) cc_final: 0.8451 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 42
  average time/residue: 0.0576
  time to fit residues: 3.7475
Evaluate side-chains
  39 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 27
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  107 VAL
Chi-restraints excluded: chain B residue  159 ASN
Chi-restraints excluded: chain B residue  271 TRP
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  485 VAL
Chi-restraints excluded: chain B residue  494 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 52 optimal weight:   10.0000
   chunk 56 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 45 optimal weight:   20.0000
   chunk 22 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 54 optimal weight:   20.0000
   chunk 63 optimal weight:    2.9990
   overall best weight:    3.7388

-------------------------------------------------------------------------------
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 = 0.3901 r_free = 0.3901 target = 0.046088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.037120 restraints weight = 105142.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.038065 restraints weight = 60613.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.038692 restraints weight = 40668.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.039112 restraints weight = 30367.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.039384 restraints weight = 24614.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.6452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6714  Z= 0.143
  Angle     :  0.575   7.896   9141  Z= 0.296
  Chirality :  0.041   0.191    965
  Planarity :  0.004   0.037   1171
  Dihedral  :  4.454  19.686    984
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 11.37 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.30), residues: 787
  helix:  0.70 (0.25), residues: 404
  sheet:  1.40 (0.78), residues: 43
  loop : -0.30 (0.36), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 494 
 TYR   0.014   0.001   TYR B 385 
 PHE   0.012   0.001   PHE B 315 
 TRP   0.011   0.001   TRP B 478 
 HIS   0.006   0.001   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6701)
  covalent geometry    : angle       0.57024 ( 9109)
  SS BOND              : bond        0.00302 (    7)
  SS BOND              : angle       0.71074 (   14)
  hydrogen bonds       : bond        0.03832 (  315)
  hydrogen bonds       : angle       4.94624 (  879)
  link_NAG-ASN         : bond        0.00139 (    6)
  link_NAG-ASN         : angle       1.74918 (   18)

*********************** 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: 16
    poor density    : 27
  time to evaluate  : 0.285 
Fit side-chains
REVERT: B  190 MET cc_start: 0.4810 (ppp) cc_final: 0.4596 (ppp)
REVERT: B  270 MET cc_start: 0.0330 (mmm) cc_final: -0.1904 (mmm)
REVERT: B  271 TRP cc_start: -0.0123 (OUTLIER) cc_final: -0.1840 (m-90)
REVERT: B  339 VAL cc_start: 0.3166 (OUTLIER) cc_final: 0.2733 (m)
REVERT: B  455 MET cc_start: 0.5053 (tmt) cc_final: 0.4813 (ttp)
REVERT: B  474 MET cc_start: 0.0228 (mmp) cc_final: -0.0060 (mmp)
REVERT: B  485 VAL cc_start: 0.5895 (OUTLIER) cc_final: 0.5155 (t)
REVERT: B  572 ASN cc_start: 0.8928 (m-40) cc_final: 0.8579 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 42
  average time/residue: 0.0565
  time to fit residues: 3.7700
Evaluate side-chains
  40 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 26
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
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  271 TRP
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  485 VAL
Chi-restraints excluded: chain B residue  494 ASP
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  581 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 74 optimal weight:   30.0000
   chunk 30 optimal weight:    7.9990
   chunk 70 optimal weight:    9.9990
   chunk 25 optimal weight:    0.7980
   chunk 66 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 76 optimal weight:   30.0000
   overall best weight:    5.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 277 ASN
B 524 GLN
B 586 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.045235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.035976 restraints weight = 106403.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.036824 restraints weight = 63523.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.037399 restraints weight = 43897.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.037781 restraints weight = 33516.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.038041 restraints weight = 27645.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.7370

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= 0.192
  Angle     :  0.653   8.214   9141  Z= 0.337
  Chirality :  0.044   0.246    965
  Planarity :  0.005   0.038   1171
  Dihedral  :  5.084  23.586    984
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 21.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 11.37 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.30), residues: 787
  helix:  0.36 (0.25), residues: 403
  sheet:  1.03 (0.76), residues: 45
  loop : -0.48 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 463 
 TYR   0.014   0.002   TYR B  50 
 PHE   0.014   0.002   PHE A 368 
 TRP   0.017   0.002   TRP B 275 
 HIS   0.008   0.002   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 6701)
  covalent geometry    : angle       0.64017 ( 9109)
  SS BOND              : bond        0.00384 (    7)
  SS BOND              : angle       0.88036 (   14)
  hydrogen bonds       : bond        0.04226 (  315)
  hydrogen bonds       : angle       5.32028 (  879)
  link_NAG-ASN         : bond        0.00196 (    6)
  link_NAG-ASN         : angle       2.92129 (   18)

*********************** 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
  44 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 25
  time to evaluate  : 0.227 
Fit side-chains
REVERT: B  270 MET cc_start: 0.2117 (mmm) cc_final: -0.0868 (mmm)
REVERT: B  271 TRP cc_start: -0.0398 (OUTLIER) cc_final: -0.1852 (m-90)
REVERT: B  339 VAL cc_start: 0.4049 (OUTLIER) cc_final: 0.3738 (t)
REVERT: B  485 VAL cc_start: 0.5316 (OUTLIER) cc_final: 0.4408 (t)
REVERT: B  512 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7482 (t80)
REVERT: B  572 ASN cc_start: 0.8709 (m-40) cc_final: 0.8384 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 43
  average time/residue: 0.0663
  time to fit residues: 4.3246
Evaluate side-chains
  40 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 24
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
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  339 VAL
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  485 VAL
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  534 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 34 optimal weight:   20.0000
   chunk 28 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 23 optimal weight:    8.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 290 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.045527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.037937 restraints weight = 91432.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.038747 restraints weight = 54079.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.039286 restraints weight = 36252.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.039624 restraints weight = 26905.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.039865 restraints weight = 21775.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.7821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6714  Z= 0.193
  Angle     :  0.652   7.744   9141  Z= 0.340
  Chirality :  0.044   0.276    965
  Planarity :  0.005   0.038   1171
  Dihedral  :  5.229  23.034    984
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 21.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.94 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.30), residues: 787
  helix:  0.20 (0.25), residues: 400
  sheet:  0.95 (0.75), residues: 45
  loop : -0.61 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 494 
 TYR   0.027   0.002   TYR B 237 
 PHE   0.027   0.002   PHE B 315 
 TRP   0.016   0.002   TRP B 477 
 HIS   0.007   0.002   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 6701)
  covalent geometry    : angle       0.64316 ( 9109)
  SS BOND              : bond        0.00387 (    7)
  SS BOND              : angle       0.83225 (   14)
  hydrogen bonds       : bond        0.04248 (  315)
  hydrogen bonds       : angle       5.37292 (  879)
  link_NAG-ASN         : bond        0.00247 (    6)
  link_NAG-ASN         : angle       2.49195 (   18)

*********************** 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  : 0.167 
Fit side-chains
REVERT: B  270 MET cc_start: 0.2546 (mmm) cc_final: 0.0843 (mmm)
REVERT: B  271 TRP cc_start: 0.0683 (OUTLIER) cc_final: -0.1551 (m-90)
REVERT: B  512 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7132 (t80)
REVERT: B  572 ASN cc_start: 0.8829 (m-40) cc_final: 0.8425 (t0)
  outliers start: 15
  outliers final: 11
  residues processed: 38
  average time/residue: 0.0672
  time to fit residues: 3.9350
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  : 0.259 
-------------------------------------------------------------------------------
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  494 ASP
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    0.0970
   chunk 54 optimal weight:   20.0000
   chunk 63 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 69 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 34 optimal weight:   20.0000
   chunk 18 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   overall best weight:    5.2186

-------------------------------------------------------------------------------
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 = 0.3882 r_free = 0.3882 target = 0.045608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.038017 restraints weight = 92264.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.038823 restraints weight = 54609.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.039366 restraints weight = 36569.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.039719 restraints weight = 27093.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.039924 restraints weight = 21790.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.8088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   6714  Z= 0.188
  Angle     :  0.685  16.760   9141  Z= 0.349
  Chirality :  0.044   0.276    965
  Planarity :  0.004   0.036   1171
  Dihedral  :  5.425  34.415    984
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 21.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 12.66 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.30), residues: 787
  helix:  0.15 (0.25), residues: 408
  sheet:  0.99 (0.74), residues: 45
  loop : -0.60 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 494 
 TYR   0.025   0.002   TYR B 237 
 PHE   0.021   0.002   PHE B 315 
 TRP   0.014   0.002   TRP B 275 
 HIS   0.007   0.002   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 6701)
  covalent geometry    : angle       0.67642 ( 9109)
  SS BOND              : bond        0.00369 (    7)
  SS BOND              : angle       0.80179 (   14)
  hydrogen bonds       : bond        0.04375 (  315)
  hydrogen bonds       : angle       5.39477 (  879)
  link_NAG-ASN         : bond        0.00131 (    6)
  link_NAG-ASN         : angle       2.55891 (   18)

*********************** 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
  39 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 25
  time to evaluate  : 0.287 
Fit side-chains
REVERT: B  270 MET cc_start: 0.3080 (mmm) cc_final: 0.1628 (mmm)
REVERT: B  271 TRP cc_start: 0.0834 (OUTLIER) cc_final: -0.1422 (m-90)
REVERT: B  376 MET cc_start: 0.8069 (ttm) cc_final: 0.7840 (ptm)
REVERT: B  512 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.6849 (t80)
REVERT: B  572 ASN cc_start: 0.8593 (m-40) cc_final: 0.8250 (t0)
  outliers start: 14
  outliers final: 10
  residues processed: 38
  average time/residue: 0.0649
  time to fit residues: 3.7610
Evaluate side-chains
  36 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 24
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
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  504 PHE
Chi-restraints excluded: chain B residue  512 PHE
Chi-restraints excluded: chain B residue  534 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 49 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 42 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
** B 241 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 = 0.3904 r_free = 0.3904 target = 0.046500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.038929 restraints weight = 90170.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.039747 restraints weight = 53517.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.040291 restraints weight = 35552.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.040643 restraints weight = 26294.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.040828 restraints weight = 21275.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.8003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6714  Z= 0.138
  Angle     :  0.627  10.753   9141  Z= 0.317
  Chirality :  0.043   0.239    965
  Planarity :  0.004   0.035   1171
  Dihedral  :  5.088  36.142    984
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.52 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.30), residues: 787
  helix:  0.49 (0.26), residues: 395
  sheet:  1.19 (0.76), residues: 46
  loop : -0.46 (0.36), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 177 
 TYR   0.023   0.001   TYR B 237 
 PHE   0.017   0.001   PHE B 315 
 TRP   0.014   0.001   TRP B 478 
 HIS   0.006   0.001   HIS A 501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6701)
  covalent geometry    : angle       0.62030 ( 9109)
  SS BOND              : bond        0.00249 (    7)
  SS BOND              : angle       0.68121 (   14)
  hydrogen bonds       : bond        0.03949 (  315)
  hydrogen bonds       : angle       5.25281 (  879)
  link_NAG-ASN         : bond        0.00157 (    6)
  link_NAG-ASN         : angle       2.14186 (   18)

********************** 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
  40 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 25
  time to evaluate  : 0.272 
Fit side-chains
REVERT: B  270 MET cc_start: 0.2475 (mmm) cc_final: 0.0707 (mmm)
REVERT: B  271 TRP cc_start: 0.0523 (OUTLIER) cc_final: -0.1663 (m-90)
REVERT: B  376 MET cc_start: 0.7978 (ttm) cc_final: 0.7606 (ptm)
REVERT: B  455 MET cc_start: 0.7296 (mtp) cc_final: 0.7018 (mmm)
REVERT: B  462 MET cc_start: 0.6102 (mpp) cc_final: 0.5446 (mmp)
REVERT: B  480 MET cc_start: 0.6665 (ptt) cc_final: 0.5859 (ttt)
REVERT: B  512 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7161 (t80)
REVERT: B  572 ASN cc_start: 0.8610 (m-40) cc_final: 0.8305 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 39
  average time/residue: 0.0680
  time to fit residues: 4.1060
Evaluate side-chains
  36 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 24
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
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 A residue  520 VAL
Chi-restraints excluded: chain B residue  271 TRP
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 57 optimal weight:   30.0000
   chunk 9 optimal weight:    0.7980
   chunk 62 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 76 optimal weight:   30.0000
   chunk 67 optimal weight:    0.0170
   chunk 38 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.5624

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

Flipped N/Q/H residues before XYZ refinement:
** B 241 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 = 0.3936 r_free = 0.3936 target = 0.046679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.038958 restraints weight = 89955.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.039774 restraints weight = 53224.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.040317 restraints weight = 35882.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 64)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.040666 restraints weight = 26837.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.040848 restraints weight = 21769.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.7853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059   6714  Z= 0.113
  Angle     :  0.578  10.946   9141  Z= 0.295
  Chirality :  0.042   0.179    965
  Planarity :  0.004   0.037   1171
  Dihedral  :  4.525  32.490    984
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.24 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.30), residues: 787
  helix:  0.82 (0.26), residues: 395
  sheet:  1.45 (0.78), residues: 44
  loop : -0.35 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 514 
 TYR   0.023   0.001   TYR B 237 
 PHE   0.015   0.001   PHE B 315 
 TRP   0.015   0.001   TRP B 478 
 HIS   0.005   0.001   HIS A 501 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6701)
  covalent geometry    : angle       0.57373 ( 9109)
  SS BOND              : bond        0.00188 (    7)
  SS BOND              : angle       0.61053 (   14)
  hydrogen bonds       : bond        0.03654 (  315)
  hydrogen bonds       : angle       5.00841 (  879)
  link_NAG-ASN         : bond        0.00203 (    6)
  link_NAG-ASN         : angle       1.65089 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1747.65 seconds
wall clock time: 30 minutes 44.02 seconds (1844.02 seconds total)