Starting phenix.real_space_refine
on Sun Apr 27 09:32:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yqq_39502/04_2025/8yqq_39502_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yqq_39502/04_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_39502/04_2025/8yqq_39502.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yqq_39502/04_2025/8yqq_39502.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yqq_39502/04_2025/8yqq_39502_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yqq_39502/04_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 4.03, per 1000 atoms: 0.78
  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: 1.29
  Conformation dependent library (CDL) restraints added in 678.3 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: 0.64
  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: 1.36

  Time building geometry restraints manager: 1.55 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:             2.020
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.830
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.980
-------------------------------------------------------------------------------
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  : 0.520 
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: 0.1695
  time to fit residues: 32.9768
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  : 0.554 
-------------------------------------------------------------------------------
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 = 0.064479 restraints weight = 13002.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.065870 restraints weight = 8546.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.066913 restraints weight = 5699.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
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      15.70412 (    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  : 0.608 
Fit side-chains
REVERT: A  502 ARG cc_start: 0.8324 (ptp-170) cc_final: 0.7978 (ptp-170)
REVERT: A  544 GLU cc_start: 0.8885 (mp0) cc_final: 0.8609 (mp0)
REVERT: A  547 PRO cc_start: 0.9054 (Cg_endo) cc_final: 0.8840 (Cg_exo)
REVERT: A  562 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.6929 (m170)
REVERT: A  578 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7555 (m-30)
REVERT: B  268 PRO cc_start: 0.8593 (Cg_endo) cc_final: 0.8349 (Cg_exo)
REVERT: B  384 TRP cc_start: 0.8843 (m-90) cc_final: 0.8642 (m-90)
REVERT: B  458 ASP cc_start: 0.8725 (t0) cc_final: 0.8412 (t0)
REVERT: B  463 SER cc_start: 0.8992 (t) cc_final: 0.8663 (p)
REVERT: B  488 MET cc_start: 0.8324 (mmt) cc_final: 0.6901 (mmt)
  outliers start: 22
  outliers final: 13
  residues processed: 111
  average time/residue: 0.1513
  time to fit residues: 22.5544
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  : 0.536 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.2743 r_free = 0.2743 target = 0.073412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2525 r_free = 0.2525 target = 0.062681 restraints weight = 13048.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2554 r_free = 0.2554 target = 0.064170 restraints weight = 8655.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2573 r_free = 0.2573 target = 0.065136 restraints weight = 6144.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.2569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5295  Z= 0.162
  Angle     :  0.758  22.876   7222  Z= 0.352
  Chirality :  0.054   0.658    782
  Planarity :  0.005   0.052    929
  Dihedral  :  8.534  59.460    862
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.13 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.42 %
    Favored  : 76.61 %
  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: -2.10 (0.32), residues: 645
  helix: -1.56 (0.55), residues: 63
  sheet: -1.82 (0.41), residues: 148
  loop : -1.22 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 269 
 HIS   0.012   0.002   HIS A 562 
 PHE   0.017   0.002   PHE A 577 
 TYR   0.017   0.002   TYR A 426 
 ARG   0.004   0.001   ARG B 409 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04426 (    1)
  link_NAG-ASN         : angle      15.72063 (    3)
  hydrogen bonds       : bond        0.03629 (  105)
  hydrogen bonds       : angle       6.86906 (  270)
  SS BOND              : bond        0.00360 (   18)
  SS BOND              : angle       0.86580 (   36)
  covalent geometry    : bond        0.00361 ( 5276)
  covalent geometry    : angle       0.68652 ( 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
  99 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.731 
Fit side-chains
REVERT: A  410 GLN cc_start: 0.7597 (mm110) cc_final: 0.7313 (mt0)
REVERT: A  413 ASN cc_start: 0.8482 (m-40) cc_final: 0.8234 (m-40)
REVERT: A  544 GLU cc_start: 0.8928 (mp0) cc_final: 0.8725 (mp0)
REVERT: B  157 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7621 (mt)
REVERT: B  434 VAL cc_start: 0.9100 (t) cc_final: 0.8864 (t)
REVERT: B  458 ASP cc_start: 0.8701 (t0) cc_final: 0.8380 (t0)
REVERT: B  463 SER cc_start: 0.8997 (t) cc_final: 0.8738 (p)
  outliers start: 17
  outliers final: 12
  residues processed: 93
  average time/residue: 0.1795
  time to fit residues: 21.5354
Evaluate side-chains
  86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
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  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 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=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:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0870
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.8760

-------------------------------------------------------------------------------
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 = 0.2726 r_free = 0.2726 target = 0.072692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2506 r_free = 0.2506 target = 0.061959 restraints weight = 13256.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2536 r_free = 0.2536 target = 0.063552 restraints weight = 8758.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2555 r_free = 0.2555 target = 0.064458 restraints weight = 6123.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.2553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5295  Z= 0.165
  Angle     :  0.725  22.169   7222  Z= 0.337
  Chirality :  0.053   0.648    782
  Planarity :  0.005   0.049    929
  Dihedral  :  7.883  58.035    853
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.13 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.42 %
    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: -1.85 (0.32), residues: 645
  helix: -1.26 (0.59), residues: 63
  sheet: -1.49 (0.42), residues: 148
  loop : -1.13 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 269 
 HIS   0.004   0.001   HIS B 138 
 PHE   0.019   0.002   PHE A 577 
 TYR   0.018   0.002   TYR A 426 
 ARG   0.003   0.001   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04382 (    1)
  link_NAG-ASN         : angle      15.21017 (    3)
  hydrogen bonds       : bond        0.03389 (  105)
  hydrogen bonds       : angle       6.70502 (  270)
  SS BOND              : bond        0.00393 (   18)
  SS BOND              : angle       0.81349 (   36)
  covalent geometry    : bond        0.00373 ( 5276)
  covalent geometry    : angle       0.65467 ( 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
  98 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 GLN cc_start: 0.7716 (mm110) cc_final: 0.7328 (mt0)
REVERT: A  413 ASN cc_start: 0.8475 (m-40) cc_final: 0.8214 (m-40)
REVERT: A  544 GLU cc_start: 0.8970 (mp0) cc_final: 0.8693 (mp0)
REVERT: B  157 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7653 (mt)
REVERT: B  268 PRO cc_start: 0.8537 (Cg_endo) cc_final: 0.8232 (Cg_exo)
REVERT: B  434 VAL cc_start: 0.9124 (t) cc_final: 0.8869 (t)
REVERT: B  463 SER cc_start: 0.9025 (t) cc_final: 0.8762 (p)
  outliers start: 21
  outliers final: 14
  residues processed: 92
  average time/residue: 0.1662
  time to fit residues: 20.0364
Evaluate side-chains
  85 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.072552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2502 r_free = 0.2502 target = 0.061814 restraints weight = 13269.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2531 r_free = 0.2531 target = 0.063363 restraints weight = 8827.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2550 r_free = 0.2550 target = 0.064289 restraints weight = 6178.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.2548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5295  Z= 0.165
  Angle     :  0.716  21.589   7222  Z= 0.335
  Chirality :  0.053   0.642    782
  Planarity :  0.005   0.046    929
  Dihedral  :  7.844  56.240    853
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.13 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.90 %
    Favored  : 76.61 %
  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: -1.81 (0.32), residues: 645
  helix: -1.11 (0.60), residues: 63
  sheet: -1.44 (0.42), residues: 149
  loop : -1.13 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 384 
 HIS   0.003   0.001   HIS B 138 
 PHE   0.021   0.002   PHE B 311 
 TYR   0.017   0.002   TYR A 426 
 ARG   0.003   0.000   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04393 (    1)
  link_NAG-ASN         : angle      14.84635 (    3)
  hydrogen bonds       : bond        0.03275 (  105)
  hydrogen bonds       : angle       6.66584 (  270)
  SS BOND              : bond        0.00376 (   18)
  SS BOND              : angle       0.84388 (   36)
  covalent geometry    : bond        0.00375 ( 5276)
  covalent geometry    : angle       0.64848 ( 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
  94 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 GLN cc_start: 0.7800 (mm110) cc_final: 0.7392 (mt0)
REVERT: A  413 ASN cc_start: 0.8468 (m-40) cc_final: 0.8198 (m-40)
REVERT: A  494 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7819 (pt)
REVERT: A  544 GLU cc_start: 0.8985 (mp0) cc_final: 0.8734 (mp0)
REVERT: B  157 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7641 (mt)
REVERT: B  268 PRO cc_start: 0.8542 (Cg_endo) cc_final: 0.8262 (Cg_exo)
REVERT: B  434 VAL cc_start: 0.9132 (t) cc_final: 0.8872 (t)
REVERT: B  458 ASP cc_start: 0.8802 (t0) cc_final: 0.8441 (t0)
REVERT: B  463 SER cc_start: 0.9064 (t) cc_final: 0.8798 (p)
  outliers start: 20
  outliers final: 12
  residues processed: 89
  average time/residue: 0.1446
  time to fit residues: 17.3181
Evaluate side-chains
  85 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  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  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  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:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0980
   chunk 1 optimal weight:    0.8980
   chunk 13 optimal weight:    0.2980
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0070
   chunk 58 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.3998

-------------------------------------------------------------------------------
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**
B 411 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.074810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2555 r_free = 0.2555 target = 0.064040 restraints weight = 13052.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.065638 restraints weight = 8617.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.066620 restraints weight = 6055.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3527

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= 0.112
  Angle     :  0.641  19.397   7222  Z= 0.304
  Chirality :  0.051   0.617    782
  Planarity :  0.004   0.047    929
  Dihedral  :  7.326  59.232    853
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.24 %
    Favored  : 76.96 %
  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: -1.61 (0.33), residues: 645
  helix: -0.88 (0.62), residues: 64
  sheet: -1.29 (0.42), residues: 148
  loop : -1.01 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 384 
 HIS   0.002   0.001   HIS B 169 
 PHE   0.016   0.001   PHE B 311 
 TYR   0.013   0.001   TYR A 426 
 ARG   0.002   0.000   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.03904 (    1)
  link_NAG-ASN         : angle      13.32288 (    3)
  hydrogen bonds       : bond        0.02891 (  105)
  hydrogen bonds       : angle       6.38772 (  270)
  SS BOND              : bond        0.00259 (   18)
  SS BOND              : angle       0.75750 (   36)
  covalent geometry    : bond        0.00247 ( 5276)
  covalent geometry    : angle       0.57937 ( 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
  91 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
REVERT: A  410 GLN cc_start: 0.7723 (mm110) cc_final: 0.7316 (mt0)
REVERT: A  413 ASN cc_start: 0.8443 (m-40) cc_final: 0.8189 (m-40)
REVERT: A  536 LYS cc_start: 0.8951 (mmpt) cc_final: 0.8572 (mmtt)
REVERT: A  544 GLU cc_start: 0.8936 (mp0) cc_final: 0.8722 (mp0)
REVERT: B  157 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7657 (mt)
REVERT: B  268 PRO cc_start: 0.8518 (Cg_endo) cc_final: 0.8254 (Cg_exo)
REVERT: B  458 ASP cc_start: 0.8798 (t0) cc_final: 0.8336 (t0)
REVERT: B  463 SER cc_start: 0.9080 (t) cc_final: 0.8649 (p)
  outliers start: 16
  outliers final: 10
  residues processed: 85
  average time/residue: 0.1645
  time to fit residues: 18.4839
Evaluate side-chains
  86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 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**
** A 552 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 = 0.2741 r_free = 0.2741 target = 0.073388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2525 r_free = 0.2525 target = 0.062786 restraints weight = 12854.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2548 r_free = 0.2548 target = 0.064147 restraints weight = 8770.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2565 r_free = 0.2565 target = 0.064940 restraints weight = 5959.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.2564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3595

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= 0.146
  Angle     :  0.668  20.141   7222  Z= 0.315
  Chirality :  0.052   0.623    782
  Planarity :  0.004   0.045    929
  Dihedral  :  7.430  56.855    853
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 20.77 %
    Favored  : 76.61 %
  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: -1.60 (0.32), residues: 645
  helix: -0.77 (0.63), residues: 64
  sheet: -1.27 (0.43), residues: 141
  loop : -1.04 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 384 
 HIS   0.004   0.001   HIS B 169 
 PHE   0.017   0.002   PHE B 311 
 TYR   0.015   0.002   TYR A 426 
 ARG   0.004   0.000   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04225 (    1)
  link_NAG-ASN         : angle      13.89316 (    3)
  hydrogen bonds       : bond        0.03059 (  105)
  hydrogen bonds       : angle       6.45562 (  270)
  SS BOND              : bond        0.00359 (   18)
  SS BOND              : angle       0.83596 (   36)
  covalent geometry    : bond        0.00331 ( 5276)
  covalent geometry    : angle       0.60345 ( 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
  91 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
REVERT: A  410 GLN cc_start: 0.7744 (mm110) cc_final: 0.7306 (mt0)
REVERT: A  413 ASN cc_start: 0.8443 (m-40) cc_final: 0.8195 (m-40)
REVERT: A  536 LYS cc_start: 0.8926 (mmpt) cc_final: 0.8552 (mmtt)
REVERT: A  544 GLU cc_start: 0.8972 (mp0) cc_final: 0.8750 (mp0)
REVERT: B  157 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7728 (mt)
REVERT: B  268 PRO cc_start: 0.8517 (Cg_endo) cc_final: 0.8242 (Cg_exo)
REVERT: B  408 GLN cc_start: 0.9347 (pm20) cc_final: 0.9142 (pm20)
REVERT: B  458 ASP cc_start: 0.8797 (t0) cc_final: 0.8371 (t0)
REVERT: B  463 SER cc_start: 0.9060 (t) cc_final: 0.8724 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 87
  average time/residue: 0.1656
  time to fit residues: 18.9571
Evaluate side-chains
  85 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
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  487 LYS
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  504 CYS
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  239 LEU
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:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.2731 r_free = 0.2731 target = 0.072871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2512 r_free = 0.2512 target = 0.062186 restraints weight = 13019.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2536 r_free = 0.2536 target = 0.063555 restraints weight = 8836.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2554 r_free = 0.2554 target = 0.064375 restraints weight = 6022.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.3685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5295  Z= 0.162
  Angle     :  0.688  20.459   7222  Z= 0.326
  Chirality :  0.052   0.625    782
  Planarity :  0.005   0.049    929
  Dihedral  :  7.102  56.507    849
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 21.29 %
    Favored  : 76.79 %
  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: -1.60 (0.32), residues: 645
  helix: -0.78 (0.63), residues: 64
  sheet: -1.19 (0.44), residues: 139
  loop : -1.08 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 384 
 HIS   0.004   0.001   HIS B 169 
 PHE   0.020   0.002   PHE B 311 
 TYR   0.017   0.002   TYR A 426 
 ARG   0.005   0.000   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04327 (    1)
  link_NAG-ASN         : angle      14.07542 (    3)
  hydrogen bonds       : bond        0.03129 (  105)
  hydrogen bonds       : angle       6.52800 (  270)
  SS BOND              : bond        0.00387 (   18)
  SS BOND              : angle       0.79854 (   36)
  covalent geometry    : bond        0.00367 ( 5276)
  covalent geometry    : angle       0.62402 ( 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
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
REVERT: A  397 ARG cc_start: 0.8700 (mmm160) cc_final: 0.8428 (mmp80)
REVERT: A  410 GLN cc_start: 0.7822 (mm110) cc_final: 0.7402 (mt0)
REVERT: A  413 ASN cc_start: 0.8433 (m-40) cc_final: 0.8203 (m-40)
REVERT: A  447 ARG cc_start: 0.8779 (ptm160) cc_final: 0.8380 (ptt180)
REVERT: A  536 LYS cc_start: 0.8936 (mmpt) cc_final: 0.8541 (mmtt)
REVERT: A  544 GLU cc_start: 0.8989 (mp0) cc_final: 0.8749 (mp0)
REVERT: B  157 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7730 (mt)
REVERT: B  268 PRO cc_start: 0.8536 (Cg_endo) cc_final: 0.8268 (Cg_exo)
REVERT: B  408 GLN cc_start: 0.9369 (pm20) cc_final: 0.9086 (pm20)
REVERT: B  458 ASP cc_start: 0.8786 (t0) cc_final: 0.8396 (t0)
REVERT: B  463 SER cc_start: 0.9047 (t) cc_final: 0.8766 (p)
  outliers start: 11
  outliers final: 9
  residues processed: 82
  average time/residue: 0.1767
  time to fit residues: 18.9940
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  : 0.608 
-------------------------------------------------------------------------------
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  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  239 LEU
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:    0.0370
   chunk 21 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0470
   chunk 12 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.4156

-------------------------------------------------------------------------------
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 = 0.2773 r_free = 0.2773 target = 0.074898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2560 r_free = 0.2560 target = 0.064300 restraints weight = 12941.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.065733 restraints weight = 8737.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.066621 restraints weight = 5859.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.2600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.3788

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= 0.113
  Angle     :  0.649  18.734   7222  Z= 0.309
  Chirality :  0.051   0.600    782
  Planarity :  0.004   0.046    929
  Dihedral  :  6.366  56.475    845
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 20.94 %
    Favored  : 76.44 %
  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: -1.53 (0.33), residues: 645
  helix: -0.72 (0.64), residues: 64
  sheet: -1.09 (0.44), residues: 139
  loop : -1.05 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 384 
 HIS   0.001   0.000   HIS B 138 
 PHE   0.020   0.001   PHE B 311 
 TYR   0.013   0.001   TYR A 426 
 ARG   0.004   0.000   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.03880 (    1)
  link_NAG-ASN         : angle      12.90731 (    3)
  hydrogen bonds       : bond        0.02790 (  105)
  hydrogen bonds       : angle       6.32511 (  270)
  SS BOND              : bond        0.00247 (   18)
  SS BOND              : angle       0.68035 (   36)
  covalent geometry    : bond        0.00250 ( 5276)
  covalent geometry    : angle       0.59265 ( 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
  92 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
REVERT: A  397 ARG cc_start: 0.8647 (mmm160) cc_final: 0.8399 (mmp80)
REVERT: A  410 GLN cc_start: 0.7726 (mm110) cc_final: 0.7324 (mt0)
REVERT: A  413 ASN cc_start: 0.8442 (m-40) cc_final: 0.8204 (m-40)
REVERT: A  447 ARG cc_start: 0.8758 (ptm160) cc_final: 0.8395 (ptt180)
REVERT: A  536 LYS cc_start: 0.8904 (mmpt) cc_final: 0.8543 (mmtt)
REVERT: A  544 GLU cc_start: 0.8961 (mp0) cc_final: 0.8755 (mp0)
REVERT: B  157 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7744 (mt)
REVERT: B  268 PRO cc_start: 0.8553 (Cg_endo) cc_final: 0.8294 (Cg_exo)
REVERT: B  408 GLN cc_start: 0.9336 (pm20) cc_final: 0.9026 (pm20)
REVERT: B  458 ASP cc_start: 0.8764 (t0) cc_final: 0.8423 (t0)
REVERT: B  463 SER cc_start: 0.9028 (t) cc_final: 0.8758 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 85
  average time/residue: 0.1658
  time to fit residues: 18.5405
Evaluate side-chains
  85 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 LEU
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  526 SER
Chi-restraints excluded: chain A residue  535 GLN
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  239 LEU
Chi-restraints excluded: chain B residue  361 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.2730 r_free = 0.2730 target = 0.072653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2512 r_free = 0.2512 target = 0.062013 restraints weight = 13155.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2538 r_free = 0.2538 target = 0.063427 restraints weight = 8845.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2551 r_free = 0.2551 target = 0.064021 restraints weight = 5953.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.2549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.3814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5295  Z= 0.152
  Angle     :  0.684  19.772   7222  Z= 0.323
  Chirality :  0.052   0.614    782
  Planarity :  0.004   0.045    929
  Dihedral  :  6.748  56.370    845
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 21.82 %
    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: -1.57 (0.32), residues: 645
  helix: -0.78 (0.63), residues: 64
  sheet: -1.09 (0.44), residues: 137
  loop : -1.09 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 269 
 HIS   0.003   0.001   HIS B 169 
 PHE   0.016   0.001   PHE B 311 
 TYR   0.016   0.002   TYR A 426 
 ARG   0.006   0.000   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04209 (    1)
  link_NAG-ASN         : angle      13.61916 (    3)
  hydrogen bonds       : bond        0.03030 (  105)
  hydrogen bonds       : angle       6.39202 (  270)
  SS BOND              : bond        0.00353 (   18)
  SS BOND              : angle       0.86767 (   36)
  covalent geometry    : bond        0.00344 ( 5276)
  covalent geometry    : angle       0.62352 ( 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
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: A  397 ARG cc_start: 0.8660 (mmm160) cc_final: 0.8428 (mmp80)
REVERT: A  413 ASN cc_start: 0.8456 (m-40) cc_final: 0.8205 (m-40)
REVERT: A  447 ARG cc_start: 0.8782 (ptm160) cc_final: 0.8394 (ptt180)
REVERT: A  536 LYS cc_start: 0.8916 (mmpt) cc_final: 0.8548 (mmtt)
REVERT: A  544 GLU cc_start: 0.8983 (mp0) cc_final: 0.8745 (mp0)
REVERT: B  157 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7790 (mt)
REVERT: B  268 PRO cc_start: 0.8582 (Cg_endo) cc_final: 0.8293 (Cg_exo)
REVERT: B  458 ASP cc_start: 0.8812 (t0) cc_final: 0.8428 (t0)
REVERT: B  463 SER cc_start: 0.8992 (t) cc_final: 0.8747 (p)
  outliers start: 11
  outliers final: 10
  residues processed: 82
  average time/residue: 0.1689
  time to fit residues: 18.1019
Evaluate side-chains
  85 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 LEU
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  535 GLN
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  239 LEU
Chi-restraints excluded: chain B residue  361 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 38 optimal weight:    0.4980
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.2735 r_free = 0.2735 target = 0.072861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2517 r_free = 0.2517 target = 0.062169 restraints weight = 13236.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2545 r_free = 0.2545 target = 0.063727 restraints weight = 8852.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2560 r_free = 0.2560 target = 0.064387 restraints weight = 5826.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.2558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
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     :  0.676  19.670   7222  Z= 0.321
  Chirality :  0.052   0.614    782
  Planarity :  0.004   0.045    929
  Dihedral  :  6.731  56.403    845
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 21.99 %
    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: -1.58 (0.32), residues: 645
  helix: -0.79 (0.63), residues: 64
  sheet: -1.11 (0.43), residues: 139
  loop : -1.08 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 380 
 HIS   0.003   0.001   HIS B 169 
 PHE   0.017   0.001   PHE B 311 
 TYR   0.015   0.001   TYR A 426 
 ARG   0.006   0.000   ARG B 470 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.04166 (    1)
  link_NAG-ASN         : angle      13.55665 (    3)
  hydrogen bonds       : bond        0.02970 (  105)
  hydrogen bonds       : angle       6.40141 (  270)
  SS BOND              : bond        0.00337 (   18)
  SS BOND              : angle       0.81614 (   36)
  covalent geometry    : bond        0.00327 ( 5276)
  covalent geometry    : angle       0.61546 ( 7183)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1909.96 seconds
wall clock time: 34 minutes 4.87 seconds (2044.87 seconds total)