Starting phenix.real_space_refine
on Sat May 10 05:43:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yqq_39502/05_2025/8yqq_39502_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yqq_39502/05_2025/8yqq_39502.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yqq_39502/05_2025/8yqq_39502.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yqq_39502/05_2025/8yqq_39502.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yqq_39502/05_2025/8yqq_39502_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yqq_39502/05_2025/8yqq_39502_trim.cif"
  }
  resolution = 3.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.031
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      47      5.16       5
     C    3217      2.51       5
     N     883      2.21       5
     O     994      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5141
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2218
          Classifications: {'peptide': 285}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 267}
    Chain: "B"
      Number of atoms: 2833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2833
          Classifications: {'peptide': 364}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 346}
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 60
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 30
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.89, per 1000 atoms: 0.76
  Number of scatterers: 5141
  At special positions: 0
  Unit cell: (68.04, 80.19, 134.46, 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      47     16.00
     O     994      8.00
     N     883      7.00
     C    3217      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 327 " - pdb=" SG  CYS A 352 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 370 " - pdb=" SG  CYS A 423 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 603 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 466 " - pdb=" SG  CYS A 546 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 495 " distance=1.99
    Simple disulfide: pdb=" SG  CYS A 476 " - pdb=" SG  CYS A 565 " distance=1.99
    Simple disulfide: pdb=" SG  CYS A 485 " - pdb=" SG  CYS A 516 " distance=1.98
    Simple disulfide: pdb=" SG  CYS A 504 " - pdb=" SG  CYS A 518 " distance=1.99
    Simple disulfide: pdb=" SG  CYS A 520 " - pdb=" SG  CYS A 533 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 556 " - pdb=" SG  CYS A 567 " distance=2.00
    Simple disulfide: pdb=" SG  CYS A 580 " - pdb=" SG  CYS A 586 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 231 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 185 " - pdb=" SG  CYS B 241 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 244 " - pdb=" SG  CYS B 365 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 281 " - pdb=" SG  CYS B 297 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 410 " - pdb=" SG  CYS B 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 437 " - pdb=" SG  CYS B 465 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 703 " - " ASN A 355 "
  Time building additional restraints: 1.41
  Conformation dependent library (CDL) restraints added in 643.8 milliseconds
  

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1204

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 12 sheets defined
      13.4% alpha, 23.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 328 through 334
      removed outlier: 3.681A  pdb=" N   TRP A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 344
      removed outlier: 4.023A  pdb=" N   TRP A 344 " --> pdb=" O   PRO A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 362
    Processing helix  chain 'A' and resid 394 through 402
      removed outlier: 3.720A  pdb=" N   ARG A 398 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
      removed outlier: 4.959A  pdb=" N   ASP A 399 " --> pdb=" O   ARG A 396 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASP A 400 " --> pdb=" O   ARG A 397 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 401 " --> pdb=" O   ARG A 398 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLN A 402 " --> pdb=" O   ASP A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 413
    Processing helix  chain 'A' and resid 430 through 434
      removed outlier: 4.180A  pdb=" N   VAL A 434 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 483
      removed outlier: 3.708A  pdb=" N   VAL A 482 " --> pdb=" O   ASP A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 572
      removed outlier: 4.097A  pdb=" N   PHE A 572 " --> pdb=" O   PRO A 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 147
    Processing helix  chain 'B' and resid 177 through 187
      removed outlier: 3.951A  pdb=" N   GLY B 181 " --> pdb=" O   ASN B 177 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA B 183 " --> pdb=" O   ASN B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 411
    Processing helix  chain 'B' and resid 480 through 491
      removed outlier: 3.519A  pdb=" N   TYR B 485 " --> pdb=" O   THR B 481 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA B 490 " --> pdb=" O   ARG B 486 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 338
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349
    Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 371
      removed outlier: 6.282A  pdb=" N   VAL A 365 " --> pdb=" O   SER A 428 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   SER A 428 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 392
      removed outlier: 3.686A  pdb=" N   PHE A 391 " --> pdb=" O   PHE A 589 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 459 through 463
      removed outlier: 4.225A  pdb=" N   ASP A 578 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   SER A 576 " --> pdb=" O   TYR A 462 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 466 through 468
      removed outlier: 4.396A  pdb=" N   CYS A 466 " --> pdb=" O   VAL A 538 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 509
      removed outlier: 6.502A  pdb=" N   THR A 509 " --> pdb=" O   LYS A 513 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   LYS A 513 " --> pdb=" O   THR A 509 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 150
      removed outlier: 3.504A  pdb=" N   ARG B 150 " --> pdb=" O   GLN B 159 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER B 167 " --> pdb=" O   SER B 162 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 196 through 200
    Processing sheet with id=AB1, first strand: chain 'B' and resid 209 through 211
    Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 275
      removed outlier: 3.744A  pdb=" N   CYS B 281 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   VAL B 275 " --> pdb=" O   HIS B 279 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   HIS B 279 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU B 348 " --> pdb=" O   VAL B 331 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   VAL B 331 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   LYS B 350 " --> pdb=" O   GLU B 329 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL B 328 " --> pdb=" O   TRP B 308 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   TRP B 308 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 378 through 383
      removed outlier: 4.250A  pdb=" N   CYS B 426 " --> pdb=" O   ILE B 405 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   VAL B 473 " --> pdb=" O   SER B 460 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER B 460 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR B 447 " --> pdb=" O   TRP B 454 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LEU B 445 " --> pdb=" O   ILE B 456 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER B 382 " --> pdb=" O   PRO B 444 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   SER B 448 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   LEU B 378 " --> pdb=" O   SER B 448 " (cutoff:3.500A)

    109 hydrogen bonds defined for protein.
    270 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: 1.61

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 885
        1.32 -     1.45: 1510
        1.45 -     1.57: 2825
        1.57 -     1.70: 0
        1.70 -     1.83: 56
  Bond restraints: 5276
  Sorted by residual:
  bond pdb=" CA  SER A 563 "
       pdb=" CB  SER A 563 "
    ideal  model  delta    sigma   weight residual
    1.533  1.450  0.083 1.69e-02 3.50e+03 2.40e+01
  bond pdb=" C   PRO A 496 "
       pdb=" O   PRO A 496 "
    ideal  model  delta    sigma   weight residual
    1.233  1.194  0.039 9.90e-03 1.02e+04 1.56e+01
  bond pdb=" N   ILE A 588 "
       pdb=" CA  ILE A 588 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.11e-02 8.12e+03 1.45e+01
  bond pdb=" CA  SER A 488 "
       pdb=" CB  SER A 488 "
    ideal  model  delta    sigma   weight residual
    1.531  1.476  0.055 1.53e-02 4.27e+03 1.31e+01
  bond pdb=" C   PRO A 490 "
       pdb=" O   PRO A 490 "
    ideal  model  delta    sigma   weight residual
    1.240  1.200  0.040 1.12e-02 7.97e+03 1.30e+01
  ... (remaining 5271 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 6625
        2.37 -     4.74: 479
        4.74 -     7.11: 65
        7.11 -     9.48: 11
        9.48 -    11.85: 3
  Bond angle restraints: 7183
  Sorted by residual:
  angle pdb=" N   ARG A 447 "
        pdb=" CA  ARG A 447 "
        pdb=" C   ARG A 447 "
      ideal   model   delta    sigma   weight residual
     113.50  103.12   10.38 1.23e+00 6.61e-01 7.12e+01
  angle pdb=" N   PRO A 475 "
        pdb=" CA  PRO A 475 "
        pdb=" C   PRO A 475 "
      ideal   model   delta    sigma   weight residual
     113.75  104.29    9.46 1.49e+00 4.50e-01 4.03e+01
  angle pdb=" C   THR A 602 "
        pdb=" CA  THR A 602 "
        pdb=" CB  THR A 602 "
      ideal   model   delta    sigma   weight residual
     111.74  103.25    8.49 1.37e+00 5.33e-01 3.84e+01
  angle pdb=" N   GLN A 559 "
        pdb=" CA  GLN A 559 "
        pdb=" C   GLN A 559 "
      ideal   model   delta    sigma   weight residual
     113.41  106.01    7.40 1.22e+00 6.72e-01 3.68e+01
  angle pdb=" CA  HIS A 562 "
        pdb=" CB  HIS A 562 "
        pdb=" CG  HIS A 562 "
      ideal   model   delta    sigma   weight residual
     113.80  119.33   -5.53 1.00e+00 1.00e+00 3.06e+01
  ... (remaining 7178 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.97: 2963
       23.97 -    47.94: 241
       47.94 -    71.91: 41
       71.91 -    95.87: 6
       95.87 -   119.84: 4
  Dihedral angle restraints: 3255
    sinusoidal: 1380
      harmonic: 1875
  Sorted by residual:
  dihedral pdb=" CD  ARG A 517 "
           pdb=" NE  ARG A 517 "
           pdb=" CZ  ARG A 517 "
           pdb=" NH1 ARG A 517 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.60  -86.60     1      1.00e+01 1.00e-02 9.03e+01
  dihedral pdb=" CB  CYS A 485 "
           pdb=" SG  CYS A 485 "
           pdb=" SG  CYS A 516 "
           pdb=" CB  CYS A 516 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.79  -63.79     1      1.00e+01 1.00e-02 5.36e+01
  dihedral pdb=" CD  ARG A 585 "
           pdb=" NE  ARG A 585 "
           pdb=" CZ  ARG A 585 "
           pdb=" NH1 ARG A 585 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   60.32  -60.32     1      1.00e+01 1.00e-02 4.85e+01
  ... (remaining 3252 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 560
       0.069 -    0.139: 171
       0.139 -    0.208: 43
       0.208 -    0.278: 7
       0.278 -    0.347: 1
  Chirality restraints: 782
  Sorted by residual:
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 355 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.75    0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" CA  ARG A 447 "
            pdb=" N   ARG A 447 "
            pdb=" C   ARG A 447 "
            pdb=" CB  ARG A 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  ASN A 598 "
            pdb=" N   ASN A 598 "
            pdb=" C   ASN A 598 "
            pdb=" CB  ASN A 598 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 779 not shown)

  Planarity restraints: 930
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 355 "    0.115 2.00e-02 2.50e+03   4.11e-01 2.11e+03
        pdb=" CG  ASN A 355 "   -0.068 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 355 "    0.401 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 355 "   -0.756 2.00e-02 2.50e+03
        pdb=" C1  NAG A 703 "    0.308 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 502 "    0.347 2.00e-02 2.50e+03   2.99e-01 1.12e+03
        pdb=" C7  NAG B 502 "   -0.084 2.00e-02 2.50e+03
        pdb=" C8  NAG B 502 "    0.129 2.00e-02 2.50e+03
        pdb=" N2  NAG B 502 "   -0.532 2.00e-02 2.50e+03
        pdb=" O7  NAG B 502 "    0.140 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 701 "   -0.346 2.00e-02 2.50e+03   2.98e-01 1.11e+03
        pdb=" C7  NAG A 701 "    0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG A 701 "   -0.113 2.00e-02 2.50e+03
        pdb=" N2  NAG A 701 "    0.531 2.00e-02 2.50e+03
        pdb=" O7  NAG A 701 "   -0.156 2.00e-02 2.50e+03
  ... (remaining 927 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.14: 3
        2.14 -     2.83: 1695
        2.83 -     3.52: 6799
        3.52 -     4.21: 12060
        4.21 -     4.90: 19794
  Nonbonded interactions: 40351
  Sorted by model distance:
  nonbonded pdb=" O3  NAG B 501 "
            pdb=" O5  NAG B 502 "
     model   vdw
     1.447 3.040
  nonbonded pdb=" O   ASN A 605 "
            pdb=" N   LEU A 607 "
     model   vdw
     1.913 3.120
  nonbonded pdb=" O3  NAG B 501 "
            pdb=" C1  NAG B 502 "
     model   vdw
     2.079 3.470
  nonbonded pdb=" OE1 GLU B 178 "
            pdb=" OG  SER B 197 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OE2 GLU B 299 "
            pdb=" OH  TYR B 337 "
     model   vdw
     2.263 3.040
  ... (remaining 40346 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:             2.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.320
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
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      :  0.021   1.439   5295  Z= 1.127
  Angle     :  1.322  22.502   7222  Z= 0.841
  Chirality :  0.073   0.347    782
  Planarity :  0.036   0.495    929
  Dihedral  : 17.141 119.842   1997
  Min Nonbonded Distance : 1.447

Molprobity Statistics.
  All-atom Clashscore : 16.88
  Ramachandran Plot:
    Outliers :  2.79 %
    Allowed  :  9.92 %
    Favored  : 87.29 %
  Rotamer:
    Outliers :  8.03 %
    Allowed  : 12.39 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.12 (0.30), residues: 645
  helix: -3.36 (0.40), residues: 69
  sheet: -0.95 (0.47), residues: 132
  loop : -2.37 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 269 
 HIS   0.006   0.001   HIS A 562 
 PHE   0.026   0.002   PHE A 383 
 TYR   0.031   0.002   TYR A 501 
 ARG   0.012   0.001   ARG B 409 

Details of bonding type rmsd
  link_NAG-ASN         : bond        1.43891 (    1)
  link_NAG-ASN         : angle      13.78990 (    3)
  hydrogen bonds       : bond        0.25193 (  105)
  hydrogen bonds       : angle      10.52951 (  270)
  SS BOND              : bond        0.02316 (   18)
  SS BOND              : angle       2.50735 (   36)
  covalent geometry    : bond        0.00801 ( 5276)
  covalent geometry    : angle       1.28280 ( 7183)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 120
  time to evaluate  : 0.621 
Fit side-chains
REVERT: A  337 SER cc_start: 0.9441 (m) cc_final: 0.9094 (t)
REVERT: A  410 GLN cc_start: 0.7969 (mm110) cc_final: 0.7715 (mt0)
REVERT: A  517 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7787 (mtm-85)
REVERT: A  538 VAL cc_start: 0.9538 (OUTLIER) cc_final: 0.9338 (t)
REVERT: A  544 GLU cc_start: 0.8893 (mp0) cc_final: 0.8644 (mp0)
REVERT: A  552 ASN cc_start: 0.9140 (t0) cc_final: 0.8784 (t0)
REVERT: A  581 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8177 (mt)
REVERT: A  602 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8770 (t)
REVERT: A  604 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8202 (m)
REVERT: A  606 ASP cc_start: 0.8625 (m-30) cc_final: 0.8352 (m-30)
REVERT: B  268 PRO cc_start: 0.8464 (Cg_endo) cc_final: 0.8187 (Cg_exo)
REVERT: B  463 SER cc_start: 0.8674 (t) cc_final: 0.8389 (p)
  outliers start: 46
  outliers final: 24
  residues processed: 150
  average time/residue: 0.1614
  time to fit residues: 31.2789
Evaluate side-chains
  115 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 86
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  444 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  465 HIS
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  488 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  513 LYS
Chi-restraints excluded: chain A residue  516 CYS
Chi-restraints excluded: chain A residue  517 ARG
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  531 ASN
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  556 CYS
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  568 SER
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  604 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0970
   chunk 58 optimal weight:    0.4980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 ASN
A 562 HIS
A 587 ASN
A 598 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.075060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2573 r_free = 0.2573 target = 0.064474 restraints weight = 13002.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.065873 restraints weight = 8557.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2617 r_free = 0.2617 target = 0.066756 restraints weight = 5698.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5295  Z= 0.149
  Angle     :  0.785  23.981   7222  Z= 0.364
  Chirality :  0.053   0.595    782
  Planarity :  0.005   0.059    929
  Dihedral  :  9.515  57.610    893
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.51 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 17.63 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.31), residues: 645
  helix: -2.52 (0.44), residues: 70
  sheet: -1.68 (0.41), residues: 155
  loop : -1.62 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 269 
 HIS   0.004   0.001   HIS B 227 
 PHE   0.022   0.002   PHE A 577 
 TYR   0.021   0.002   TYR A 426 
 ARG   0.005   0.001   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04073 (    1)
  link_NAG-ASN         : angle      15.70413 (    3)
  hydrogen bonds       : bond        0.03914 (  105)
  hydrogen bonds       : angle       7.26431 (  270)
  SS BOND              : bond        0.00354 (   18)
  SS BOND              : angle       0.88897 (   36)
  covalent geometry    : bond        0.00321 ( 5276)
  covalent geometry    : angle       0.71560 ( 7183)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.546 
Fit side-chains
REVERT: A  502 ARG cc_start: 0.8323 (ptp-170) cc_final: 0.7975 (ptp-170)
REVERT: A  544 GLU cc_start: 0.8886 (mp0) cc_final: 0.8609 (mp0)
REVERT: A  547 PRO cc_start: 0.9051 (Cg_endo) cc_final: 0.8840 (Cg_exo)
REVERT: A  562 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.6929 (m170)
REVERT: A  578 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7555 (m-30)
REVERT: B  268 PRO cc_start: 0.8593 (Cg_endo) cc_final: 0.8351 (Cg_exo)
REVERT: B  384 TRP cc_start: 0.8842 (m-90) cc_final: 0.8642 (m-90)
REVERT: B  458 ASP cc_start: 0.8720 (t0) cc_final: 0.8408 (t0)
REVERT: B  463 SER cc_start: 0.8988 (t) cc_final: 0.8659 (p)
REVERT: B  488 MET cc_start: 0.8316 (mmt) cc_final: 0.6891 (mmt)
  outliers start: 22
  outliers final: 13
  residues processed: 111
  average time/residue: 0.1428
  time to fit residues: 21.2129
Evaluate side-chains
  90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  531 ASN
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  607 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0270
   chunk 3 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 372 ASN
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 552 ASN
A 595 ASN
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.074742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2558 r_free = 0.2558 target = 0.064048 restraints weight = 13074.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2586 r_free = 0.2586 target = 0.065566 restraints weight = 8561.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.066547 restraints weight = 6057.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5295  Z= 0.134
  Angle     :  0.733  22.009   7222  Z= 0.339
  Chirality :  0.053   0.648    782
  Planarity :  0.005   0.053    929
  Dihedral  :  8.194  59.265    862
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.67 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.90 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.32), residues: 645
  helix: -1.85 (0.52), residues: 69
  sheet: -1.72 (0.40), residues: 156
  loop : -1.18 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 269 
 HIS   0.010   0.001   HIS A 562 
 PHE   0.016   0.002   PHE A 577 
 TYR   0.016   0.001   TYR A 426 
 ARG   0.004   0.000   ARG B 409 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04170 (    1)
  link_NAG-ASN         : angle      15.06038 (    3)
  hydrogen bonds       : bond        0.03481 (  105)
  hydrogen bonds       : angle       6.75877 (  270)
  SS BOND              : bond        0.00284 (   18)
  SS BOND              : angle       0.81144 (   36)
  covalent geometry    : bond        0.00291 ( 5276)
  covalent geometry    : angle       0.66450 ( 7183)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A  413 ASN cc_start: 0.8393 (m-40) cc_final: 0.8133 (m-40)
REVERT: A  544 GLU cc_start: 0.8915 (mp0) cc_final: 0.8674 (mp0)
REVERT: B  384 TRP cc_start: 0.8894 (m-90) cc_final: 0.8674 (m-90)
REVERT: B  458 ASP cc_start: 0.8680 (t0) cc_final: 0.8297 (t0)
REVERT: B  463 SER cc_start: 0.9007 (t) cc_final: 0.8721 (p)
  outliers start: 17
  outliers final: 10
  residues processed: 98
  average time/residue: 0.1540
  time to fit residues: 19.9808
Evaluate side-chains
  84 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0670
   chunk 51 optimal weight:    8.9990
   chunk 33 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.074042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2538 r_free = 0.2538 target = 0.063361 restraints weight = 13249.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.064930 restraints weight = 8730.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2586 r_free = 0.2586 target = 0.065836 restraints weight = 6158.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5295  Z= 0.137
  Angle     :  0.695  21.223   7222  Z= 0.324
  Chirality :  0.053   0.643    782
  Planarity :  0.004   0.051    929
  Dihedral  :  7.533  59.510    853
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.74 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.94 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.33), residues: 645
  helix: -1.08 (0.61), residues: 63
  sheet: -1.49 (0.40), residues: 160
  loop : -1.03 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 176 
 HIS   0.006   0.001   HIS A 465 
 PHE   0.017   0.002   PHE B 311 
 TYR   0.016   0.002   TYR A 426 
 ARG   0.003   0.000   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04119 (    1)
  link_NAG-ASN         : angle      14.54573 (    3)
  hydrogen bonds       : bond        0.03212 (  105)
  hydrogen bonds       : angle       6.55727 (  270)
  SS BOND              : bond        0.00360 (   18)
  SS BOND              : angle       0.78046 (   36)
  covalent geometry    : bond        0.00304 ( 5276)
  covalent geometry    : angle       0.62828 ( 7183)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 GLN cc_start: 0.7634 (mm110) cc_final: 0.7283 (mt0)
REVERT: A  413 ASN cc_start: 0.8466 (m-40) cc_final: 0.8206 (m-40)
REVERT: A  502 ARG cc_start: 0.8544 (ptp-170) cc_final: 0.7905 (ptt180)
REVERT: A  540 VAL cc_start: 0.9487 (OUTLIER) cc_final: 0.9268 (p)
REVERT: A  544 GLU cc_start: 0.8925 (mp0) cc_final: 0.8687 (mp0)
REVERT: B  157 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7625 (mt)
REVERT: B  293 THR cc_start: 0.8680 (t) cc_final: 0.8440 (t)
REVERT: B  458 ASP cc_start: 0.8682 (t0) cc_final: 0.8341 (t0)
REVERT: B  463 SER cc_start: 0.9040 (t) cc_final: 0.8580 (p)
  outliers start: 20
  outliers final: 13
  residues processed: 94
  average time/residue: 0.1870
  time to fit residues: 22.6902
Evaluate side-chains
  88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.073002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2512 r_free = 0.2512 target = 0.062183 restraints weight = 13224.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2543 r_free = 0.2543 target = 0.063806 restraints weight = 8869.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2561 r_free = 0.2561 target = 0.064658 restraints weight = 6183.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5295  Z= 0.155
  Angle     :  0.696  21.345   7222  Z= 0.327
  Chirality :  0.053   0.641    782
  Planarity :  0.005   0.047    929
  Dihedral  :  8.117  58.470    853
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.36 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 19.90 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.32), residues: 645
  helix: -0.98 (0.61), residues: 63
  sheet: -1.34 (0.40), residues: 160
  loop : -1.07 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 269 
 HIS   0.004   0.001   HIS A 465 
 PHE   0.015   0.002   PHE B 209 
 TYR   0.017   0.002   TYR A 426 
 ARG   0.004   0.001   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04301 (    1)
  link_NAG-ASN         : angle      14.69770 (    3)
  hydrogen bonds       : bond        0.03143 (  105)
  hydrogen bonds       : angle       6.53343 (  270)
  SS BOND              : bond        0.00392 (   18)
  SS BOND              : angle       0.82661 (   36)
  covalent geometry    : bond        0.00350 ( 5276)
  covalent geometry    : angle       0.62746 ( 7183)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 GLN cc_start: 0.7683 (mm110) cc_final: 0.7303 (mt0)
REVERT: A  413 ASN cc_start: 0.8499 (m-40) cc_final: 0.8239 (m-40)
REVERT: A  544 GLU cc_start: 0.8961 (mp0) cc_final: 0.8694 (mp0)
REVERT: B  157 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7567 (mt)
REVERT: B  270 GLN cc_start: 0.9031 (tp40) cc_final: 0.8081 (tp40)
REVERT: B  458 ASP cc_start: 0.8690 (t0) cc_final: 0.8417 (t0)
REVERT: B  463 SER cc_start: 0.9082 (t) cc_final: 0.8837 (p)
  outliers start: 22
  outliers final: 14
  residues processed: 91
  average time/residue: 0.1815
  time to fit residues: 21.0088
Evaluate side-chains
  86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0040
   chunk 7 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0000
   chunk 1 optimal weight:    0.3980
   chunk 13 optimal weight:    0.0870
   chunk 16 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0970
   chunk 58 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.1172

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 227 HIS
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 411 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.077800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.067171 restraints weight = 13015.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.068817 restraints weight = 8466.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.069704 restraints weight = 5946.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   5295  Z= 0.100
  Angle     :  0.619  17.506   7222  Z= 0.296
  Chirality :  0.050   0.585    782
  Planarity :  0.004   0.047    929
  Dihedral  :  6.843  56.854    853
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.24 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.33), residues: 645
  helix: -0.81 (0.63), residues: 63
  sheet: -1.40 (0.46), residues: 129
  loop : -0.95 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 269 
 HIS   0.003   0.001   HIS A 465 
 PHE   0.011   0.001   PHE A 383 
 TYR   0.012   0.001   TYR A 426 
 ARG   0.003   0.000   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.03595 (    1)
  link_NAG-ASN         : angle      11.97581 (    3)
  hydrogen bonds       : bond        0.02654 (  105)
  hydrogen bonds       : angle       6.11338 (  270)
  SS BOND              : bond        0.00224 (   18)
  SS BOND              : angle       0.67161 (   36)
  covalent geometry    : bond        0.00214 ( 5276)
  covalent geometry    : angle       0.56804 ( 7183)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 GLN cc_start: 0.7601 (mm110) cc_final: 0.7231 (mt0)
REVERT: A  413 ASN cc_start: 0.8424 (m-40) cc_final: 0.8221 (m-40)
REVERT: A  536 LYS cc_start: 0.8901 (mmpt) cc_final: 0.8521 (mmtt)
REVERT: A  544 GLU cc_start: 0.8855 (mp0) cc_final: 0.8629 (mp0)
REVERT: B  157 ILE cc_start: 0.7978 (pt) cc_final: 0.7505 (mt)
REVERT: B  270 GLN cc_start: 0.9002 (tp40) cc_final: 0.8030 (tp40)
REVERT: B  293 THR cc_start: 0.8607 (t) cc_final: 0.8362 (t)
REVERT: B  458 ASP cc_start: 0.8622 (t0) cc_final: 0.8410 (t0)
REVERT: B  463 SER cc_start: 0.9120 (t) cc_final: 0.8845 (p)
  outliers start: 14
  outliers final: 10
  residues processed: 94
  average time/residue: 0.1590
  time to fit residues: 19.5578
Evaluate side-chains
  88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:    0.0570
   chunk 55 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 6 optimal weight:    0.1980
   chunk 17 optimal weight:    0.6980
   chunk 58 optimal weight:    0.2980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.076028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2586 r_free = 0.2586 target = 0.065517 restraints weight = 12795.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.066947 restraints weight = 8638.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.067598 restraints weight = 5817.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.3589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5295  Z= 0.116
  Angle     :  0.642  18.287   7222  Z= 0.302
  Chirality :  0.051   0.598    782
  Planarity :  0.004   0.042    929
  Dihedral  :  6.678  57.065    847
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 21.12 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.32), residues: 645
  helix: -0.76 (0.64), residues: 63
  sheet: -1.26 (0.46), residues: 129
  loop : -0.89 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 269 
 HIS   0.002   0.001   HIS A 465 
 PHE   0.015   0.001   PHE B 311 
 TYR   0.016   0.001   TYR A 528 
 ARG   0.003   0.000   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.03838 (    1)
  link_NAG-ASN         : angle      12.66095 (    3)
  hydrogen bonds       : bond        0.02763 (  105)
  hydrogen bonds       : angle       6.08664 (  270)
  SS BOND              : bond        0.00269 (   18)
  SS BOND              : angle       0.84676 (   36)
  covalent geometry    : bond        0.00262 ( 5276)
  covalent geometry    : angle       0.58585 ( 7183)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 ASN cc_start: 0.8450 (m-40) cc_final: 0.8190 (m-40)
REVERT: A  536 LYS cc_start: 0.8896 (mmpt) cc_final: 0.8526 (mmtt)
REVERT: A  544 GLU cc_start: 0.8882 (mp0) cc_final: 0.8664 (mp0)
REVERT: A  553 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8155 (mt-10)
REVERT: B  157 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7601 (mt)
REVERT: B  270 GLN cc_start: 0.9005 (tp40) cc_final: 0.8052 (tp40)
REVERT: B  293 THR cc_start: 0.8629 (t) cc_final: 0.8402 (t)
REVERT: B  458 ASP cc_start: 0.8634 (t0) cc_final: 0.8381 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 90
  average time/residue: 0.1684
  time to fit residues: 19.7717
Evaluate side-chains
  89 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0980
   chunk 49 optimal weight:    0.0970
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.075850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.065307 restraints weight = 12938.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.066757 restraints weight = 8765.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.067512 restraints weight = 5861.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.3692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5295  Z= 0.119
  Angle     :  0.649  18.327   7222  Z= 0.306
  Chirality :  0.051   0.593    782
  Planarity :  0.004   0.044    929
  Dihedral  :  6.740  56.422    847
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 21.29 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.33), residues: 645
  helix: -0.72 (0.64), residues: 63
  sheet: -1.25 (0.43), residues: 141
  loop : -0.85 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 269 
 HIS   0.002   0.001   HIS A 465 
 PHE   0.017   0.001   PHE B 311 
 TYR   0.015   0.001   TYR A 528 
 ARG   0.005   0.000   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.03881 (    1)
  link_NAG-ASN         : angle      12.66507 (    3)
  hydrogen bonds       : bond        0.02753 (  105)
  hydrogen bonds       : angle       6.06054 (  270)
  SS BOND              : bond        0.00273 (   18)
  SS BOND              : angle       0.76928 (   36)
  covalent geometry    : bond        0.00268 ( 5276)
  covalent geometry    : angle       0.59452 ( 7183)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 ASN cc_start: 0.8467 (m-40) cc_final: 0.8221 (m-40)
REVERT: A  447 ARG cc_start: 0.8761 (ptm160) cc_final: 0.8404 (ptt180)
REVERT: A  536 LYS cc_start: 0.8909 (mmpt) cc_final: 0.8522 (mmtt)
REVERT: A  544 GLU cc_start: 0.8916 (mp0) cc_final: 0.8642 (mp0)
REVERT: A  553 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8180 (mt-10)
REVERT: B  157 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7489 (mt)
REVERT: B  270 GLN cc_start: 0.8999 (tp40) cc_final: 0.8057 (tp40)
REVERT: B  293 THR cc_start: 0.8611 (t) cc_final: 0.8382 (t)
REVERT: B  458 ASP cc_start: 0.8590 (t0) cc_final: 0.8361 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 89
  average time/residue: 0.1844
  time to fit residues: 21.5834
Evaluate side-chains
  89 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0170
   chunk 31 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0670
   chunk 39 optimal weight:    1.9990
   chunk 43 optimal weight:    0.4980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.076266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.065650 restraints weight = 12939.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2617 r_free = 0.2617 target = 0.067207 restraints weight = 8756.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.067902 restraints weight = 5762.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.3774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5295  Z= 0.118
  Angle     :  0.660  18.152   7222  Z= 0.312
  Chirality :  0.051   0.587    782
  Planarity :  0.004   0.048    929
  Dihedral  :  6.732  56.461    847
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 21.47 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.33), residues: 645
  helix: -0.72 (0.64), residues: 63
  sheet: -1.17 (0.43), residues: 143
  loop : -0.89 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 269 
 HIS   0.002   0.001   HIS A 465 
 PHE   0.022   0.001   PHE B 311 
 TYR   0.014   0.001   TYR A 426 
 ARG   0.003   0.000   ARG A 397 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.03856 (    1)
  link_NAG-ASN         : angle      12.54813 (    3)
  hydrogen bonds       : bond        0.02748 (  105)
  hydrogen bonds       : angle       6.04947 (  270)
  SS BOND              : bond        0.00265 (   18)
  SS BOND              : angle       0.74221 (   36)
  covalent geometry    : bond        0.00263 ( 5276)
  covalent geometry    : angle       0.60753 ( 7183)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
REVERT: A  413 ASN cc_start: 0.8471 (m-40) cc_final: 0.8188 (m-40)
REVERT: A  447 ARG cc_start: 0.8748 (ptm160) cc_final: 0.8406 (ptt180)
REVERT: A  536 LYS cc_start: 0.8904 (mmpt) cc_final: 0.8540 (mmtt)
REVERT: A  544 GLU cc_start: 0.8898 (mp0) cc_final: 0.8628 (mp0)
REVERT: A  553 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8164 (mt-10)
REVERT: B  157 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7499 (mt)
REVERT: B  270 GLN cc_start: 0.8967 (tp40) cc_final: 0.8047 (tp40)
REVERT: B  293 THR cc_start: 0.8592 (t) cc_final: 0.8364 (t)
  outliers start: 15
  outliers final: 12
  residues processed: 83
  average time/residue: 0.2010
  time to fit residues: 21.2259
Evaluate side-chains
  86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 PHE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0020
   chunk 50 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0770
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.4146

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.075926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.065227 restraints weight = 13166.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.066695 restraints weight = 8791.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.067359 restraints weight = 5862.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.3849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5295  Z= 0.115
  Angle     :  0.653  17.809   7222  Z= 0.309
  Chirality :  0.051   0.581    782
  Planarity :  0.004   0.041    929
  Dihedral  :  6.644  56.495    847
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 21.12 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.32), residues: 645
  helix: -0.68 (0.65), residues: 64
  sheet: -1.16 (0.42), residues: 145
  loop : -0.89 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 332 
 HIS   0.002   0.001   HIS A 465 
 PHE   0.009   0.001   PHE A 383 
 TYR   0.013   0.001   TYR A 426 
 ARG   0.004   0.000   ARG A 397 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.03810 (    1)
  link_NAG-ASN         : angle      12.31849 (    3)
  hydrogen bonds       : bond        0.02753 (  105)
  hydrogen bonds       : angle       6.00317 (  270)
  SS BOND              : bond        0.00251 (   18)
  SS BOND              : angle       0.72100 (   36)
  covalent geometry    : bond        0.00257 ( 5276)
  covalent geometry    : angle       0.60176 ( 7183)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
REVERT: A  397 ARG cc_start: 0.8452 (mmm160) cc_final: 0.7284 (mmm160)
REVERT: A  413 ASN cc_start: 0.8445 (m-40) cc_final: 0.8169 (m-40)
REVERT: A  447 ARG cc_start: 0.8766 (ptm160) cc_final: 0.8428 (ptt180)
REVERT: A  536 LYS cc_start: 0.8922 (mmpt) cc_final: 0.8562 (mmtt)
REVERT: A  544 GLU cc_start: 0.8888 (mp0) cc_final: 0.8601 (mp0)
REVERT: A  553 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8157 (mt-10)
REVERT: B  157 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7504 (mt)
REVERT: B  270 GLN cc_start: 0.8958 (tp40) cc_final: 0.8033 (tp40)
REVERT: B  293 THR cc_start: 0.8563 (t) cc_final: 0.8363 (t)
  outliers start: 15
  outliers final: 12
  residues processed: 83
  average time/residue: 0.1848
  time to fit residues: 19.7659
Evaluate side-chains
  82 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 PHE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0020
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6788

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
A 424 GLN
** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.074320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2546 r_free = 0.2546 target = 0.063592 restraints weight = 13268.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.064971 restraints weight = 8901.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.065616 restraints weight = 6056.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.3849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5295  Z= 0.144
  Angle     :  0.697  18.925   7222  Z= 0.326
  Chirality :  0.052   0.591    782
  Planarity :  0.004   0.054    929
  Dihedral  :  7.085  56.485    847
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 21.47 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.32), residues: 645
  helix: -0.72 (0.64), residues: 64
  sheet: -0.91 (0.42), residues: 141
  loop : -0.91 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 380 
 HIS   0.003   0.001   HIS B 169 
 PHE   0.013   0.002   PHE B 311 
 TYR   0.017   0.002   TYR A 426 
 ARG   0.004   0.000   ARG A 397 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04095 (    1)
  link_NAG-ASN         : angle      13.03043 (    3)
  hydrogen bonds       : bond        0.02889 (  105)
  hydrogen bonds       : angle       6.13786 (  270)
  SS BOND              : bond        0.00322 (   18)
  SS BOND              : angle       0.80144 (   36)
  covalent geometry    : bond        0.00326 ( 5276)
  covalent geometry    : angle       0.64370 ( 7183)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1896.94 seconds
wall clock time: 34 minutes 2.68 seconds (2042.68 seconds total)