Starting phenix.real_space_refine
on Thu Jun  5 17:53:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wgw_37517/06_2025/8wgw_37517.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wgw_37517/06_2025/8wgw_37517.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wgw_37517/06_2025/8wgw_37517.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wgw_37517/06_2025/8wgw_37517.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wgw_37517/06_2025/8wgw_37517.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wgw_37517/06_2025/8wgw_37517.cif"
  }
  resolution = 2.9
  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=  -0.005 sd=   0.079
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4199      2.51       5
     N    1084      2.21       5
     O    1243      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6564
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1589
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 198, 1578
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
      Conformer: "B"
        Number of residues, atoms: 198, 1578
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
          bond proxies already assigned to first conformer: 1613
    Chain: "B"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {' ZN': 1, 'NAG': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 493 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 493 " occ=0.50
  Time building chain proxies: 7.56, per 1000 atoms: 1.15
  Number of scatterers: 6564
  At special positions: 0
  Unit cell: (82.016, 84.812, 119.296, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     O    1243      8.00
     N    1084      7.00
     C    4199      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
      " NAG B 701 " - " ASN B 322 "
      " NAG B 702 " - " ASN B 432 "
      " NAG B 703 " - " ASN B 103 "
      " NAG B 704 " - " ASN B  90 "
      " NAG B 705 " - " ASN B  53 "
      " NAG C   1 " - " ASN B 546 "
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1498

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 6 sheets defined
      51.6% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 364 through 368
      removed outlier: 3.588A  pdb=" N   LEU A 368 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 4.436A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'B' and resid 20 through 53
      removed outlier: 3.690A  pdb=" N   HIS B  34 " --> pdb=" O   ASP B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 81
      removed outlier: 3.613A  pdb=" N   GLN B  60 " --> pdb=" O   GLU B  56 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLN B  81 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 101
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 3.533A  pdb=" N   SER B 106 " --> pdb=" O   ASN B 103 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL B 107 " --> pdb=" O   GLY B 104 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU B 108 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 103 through 108'
    Processing helix  chain 'B' and resid 109 through 129
    Processing helix  chain 'B' and resid 145 through 155
      removed outlier: 3.670A  pdb=" N   ASN B 149 " --> pdb=" O   GLU B 145 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   ILE B 151 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   MET B 152 " --> pdb=" O   LEU B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 172
    Processing helix  chain 'B' and resid 173 through 175
      No H-bonds generated for 'chain 'B' and resid 173 through 175'
    Processing helix  chain 'B' and resid 176 through 194
      removed outlier: 3.602A  pdb=" N   VAL B 185 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 205
    Processing helix  chain 'B' and resid 220 through 227
      removed outlier: 3.709A  pdb=" N   GLU B 224 " --> pdb=" O   GLY B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 247
    Processing helix  chain 'B' and resid 293 through 300
    Processing helix  chain 'B' and resid 303 through 319
    Processing helix  chain 'B' and resid 324 through 331
      removed outlier: 3.777A  pdb=" N   TRP B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLU B 329 " --> pdb=" O   GLN B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 386
    Processing helix  chain 'B' and resid 399 through 413
      removed outlier: 3.654A  pdb=" N   ALA B 403 " --> pdb=" O   GLY B 399 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   MET B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER B 409 " --> pdb=" O   GLY B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 422
      removed outlier: 3.702A  pdb=" N   SER B 420 " --> pdb=" O   LYS B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 444
      removed outlier: 3.968A  pdb=" N   GLU B 435 " --> pdb=" O   ASP B 431 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ILE B 436 " --> pdb=" O   ASN B 432 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ASN B 437 " --> pdb=" O   GLU B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 466
    Processing helix  chain 'B' and resid 469 through 471
      No H-bonds generated for 'chain 'B' and resid 469 through 471'
    Processing helix  chain 'B' and resid 472 through 482
    Processing helix  chain 'B' and resid 498 through 502
    Processing helix  chain 'B' and resid 505 through 509
      removed outlier: 4.084A  pdb=" N   ASP B 509 " --> pdb=" O   VAL B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 532
      removed outlier: 4.258A  pdb=" N   TYR B 516 " --> pdb=" O   PHE B 512 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   PHE B 523 " --> pdb=" O   THR B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 542
      removed outlier: 3.584A  pdb=" N   LYS B 541 " --> pdb=" O   PRO B 538 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   CYS B 542 " --> pdb=" O   LEU B 539 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 538 through 542'
    Processing helix  chain 'B' and resid 547 through 559
      removed outlier: 3.794A  pdb=" N   MET B 557 " --> pdb=" O   LYS B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 572
    Processing helix  chain 'B' and resid 581 through 588
    Processing helix  chain 'B' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 448 through 454
      removed outlier: 5.757A  pdb=" N   TYR A 449 " --> pdb=" O   PHE A 497 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   PHE A 497 " --> pdb=" O   TYR A 449 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   TYR A 451 " --> pdb=" O   TYR A 495 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 132
      removed outlier: 3.820A  pdb=" N   LEU B 142 " --> pdb=" O   VAL B 132 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 263
      removed outlier: 5.928A  pdb=" N   LEU B 262 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 352
      removed outlier: 6.052A  pdb=" N   ASP B 355 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)

    289 hydrogen bonds defined for protein.
    831 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: 1.69

  Time building geometry restraints manager: 1.84 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2091
        1.34 -     1.46: 1586
        1.46 -     1.58: 3012
        1.58 -     1.69: 1
        1.69 -     1.81: 58
  Bond restraints: 6748
  Sorted by residual:
  bond pdb=" CB  PRO B 289 "
       pdb=" CG  PRO B 289 "
    ideal  model  delta    sigma   weight residual
    1.492  1.655 -0.163 5.00e-02 4.00e+02 1.06e+01
  bond pdb=" C1  NAG B 704 "
       pdb=" O5  NAG B 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.92e+00
  bond pdb=" C1  NAG B 703 "
       pdb=" O5  NAG B 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.70e+00
  bond pdb=" CA  VAL B 339 "
       pdb=" CB  VAL B 339 "
    ideal  model  delta    sigma   weight residual
    1.532  1.546 -0.014 1.08e-02 8.57e+03 1.60e+00
  bond pdb=" C2  NAG B 703 "
       pdb=" N2  NAG B 703 "
    ideal  model  delta    sigma   weight residual
    1.439  1.464 -0.025 2.00e-02 2.50e+03 1.52e+00
  ... (remaining 6743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 9068
        2.39 -     4.78: 91
        4.78 -     7.16: 8
        7.16 -     9.55: 2
        9.55 -    11.94: 2
  Bond angle restraints: 9171
  Sorted by residual:
  angle pdb=" CA  PRO B 289 "
        pdb=" N   PRO B 289 "
        pdb=" CD  PRO B 289 "
      ideal   model   delta    sigma   weight residual
     112.00  100.06   11.94 1.40e+00 5.10e-01 7.27e+01
  angle pdb=" N   PRO B 289 "
        pdb=" CD  PRO B 289 "
        pdb=" CG  PRO B 289 "
      ideal   model   delta    sigma   weight residual
     103.20   96.94    6.26 1.50e+00 4.44e-01 1.74e+01
  angle pdb=" N   VAL A 367 "
        pdb=" CA  VAL A 367 "
        pdb=" C   VAL A 367 "
      ideal   model   delta    sigma   weight residual
     112.29  108.65    3.64 9.40e-01 1.13e+00 1.50e+01
  angle pdb=" N   GLY B 466 "
        pdb=" CA  GLY B 466 "
        pdb=" C   GLY B 466 "
      ideal   model   delta    sigma   weight residual
     113.18  120.66   -7.48 2.37e+00 1.78e-01 9.96e+00
  angle pdb=" N   PRO B 289 "
        pdb=" CA  PRO B 289 "
        pdb=" C   PRO B 289 "
      ideal   model   delta    sigma   weight residual
     111.03  115.70   -4.67 1.78e+00 3.16e-01 6.87e+00
  ... (remaining 9166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.43: 3683
       21.43 -    42.85: 286
       42.85 -    64.28: 52
       64.28 -    85.70: 9
       85.70 -   107.13: 42
  Dihedral angle restraints: 4072
    sinusoidal: 1737
      harmonic: 2335
  Sorted by residual:
  dihedral pdb=" CA  ASN B 338 "
           pdb=" C   ASN B 338 "
           pdb=" N   VAL B 339 "
           pdb=" CA  VAL B 339 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.50   21.50     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" C2  NAG B 701 "
           pdb=" C3  NAG B 701 "
           pdb=" C4  NAG B 701 "
           pdb=" O4  NAG B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   67.98  107.13     1      3.00e+01 1.11e-03 1.38e+01
  dihedral pdb=" C2  NAG B 701 "
           pdb=" C3  NAG B 701 "
           pdb=" C4  NAG B 701 "
           pdb=" C5  NAG B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.78  -53.19  106.97     1      3.00e+01 1.11e-03 1.38e+01
  ... (remaining 4069 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 726
       0.045 -    0.090: 195
       0.090 -    0.135: 55
       0.135 -    0.180: 2
       0.180 -    0.225: 2
  Chirality restraints: 980
  Sorted by residual:
  chirality pdb=" CG  LEU B 267 "
            pdb=" CB  LEU B 267 "
            pdb=" CD1 LEU B 267 "
            pdb=" CD2 LEU B 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" C1  NAG B 702 "
            pdb=" ND2 ASN B 432 "
            pdb=" C2  NAG B 702 "
            pdb=" O5  NAG B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 9.30e-01
  chirality pdb=" C2  NAG B 703 "
            pdb=" C1  NAG B 703 "
            pdb=" C3  NAG B 703 "
            pdb=" N2  NAG B 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.31   -0.18 2.00e-01 2.50e+01 7.85e-01
  ... (remaining 977 not shown)

  Planarity restraints: 1186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 288 "   -0.050 5.00e-02 4.00e+02   6.99e-02 7.82e+00
        pdb=" N   PRO B 289 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO B 289 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 289 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 425 "   -0.034 5.00e-02 4.00e+02   5.19e-02 4.32e+00
        pdb=" N   PRO B 426 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B 426 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 426 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 478 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO A 479 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 479 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 479 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1183 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 204
        2.71 -     3.26: 6682
        3.26 -     3.81: 10938
        3.81 -     4.35: 13988
        4.35 -     4.90: 23629
  Nonbonded interactions: 55441
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" OE2 GLU B 166 "
            pdb=" OG  SER B 170 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" O   SER A 359 "
            pdb=" OG1 THR A 523 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" O   ILE B 358 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OD1 ASP B 382 "
            pdb=" OH  TYR B 385 "
     model   vdw
     2.256 3.040
  ... (remaining 55436 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             22.940
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.730
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.163   6757  Z= 0.149
  Angle     :  0.597  11.938   9197  Z= 0.304
  Chirality :  0.044   0.225    980
  Planarity :  0.005   0.070   1179
  Dihedral  : 19.741 107.128   2571
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.00 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.30), residues: 793
  helix:  0.73 (0.27), residues: 372
  sheet: -0.07 (0.73), residues: 57
  loop : -0.96 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 566 
 HIS   0.004   0.001   HIS B 374 
 PHE   0.011   0.001   PHE B 369 
 TYR   0.022   0.001   TYR B 381 
 ARG   0.002   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00192 (    7)
  link_NAG-ASN         : angle       1.34606 (   21)
  link_BETA1-4         : bond        0.01854 (    1)
  link_BETA1-4         : angle       2.53150 (    3)
  hydrogen bonds       : bond        0.14173 (  289)
  hydrogen bonds       : angle       6.12046 (  831)
  SS BOND              : bond        0.00093 (    1)
  SS BOND              : angle       0.08152 (    2)
  covalent geometry    : bond        0.00359 ( 6748)
  covalent geometry    : angle       0.59242 ( 9171)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.706 
Fit side-chains
REVERT: A  444 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7801 (mtpm)
REVERT: B   98 GLN cc_start: 0.7706 (tt0) cc_final: 0.7471 (tt0)
REVERT: B  227 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7206 (mt-10)
REVERT: B  383 MET cc_start: 0.9016 (mtp) cc_final: 0.8801 (mtp)
REVERT: B  597 ASP cc_start: 0.7476 (m-30) cc_final: 0.7135 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 1.2687
  time to fit residues: 158.8601
Evaluate side-chains
  90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
A 506 GLN
B  60 GLN
B 578 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.149653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.112614 restraints weight = 17711.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 3.24
r_work: 0.3130 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   6757  Z= 0.213
  Angle     :  0.691   9.562   9197  Z= 0.331
  Chirality :  0.048   0.283    980
  Planarity :  0.005   0.051   1179
  Dihedral  : 13.711  81.449   1034
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.19 %
    Favored  : 86.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.30), residues: 793
  helix:  0.66 (0.27), residues: 382
  sheet: -0.13 (0.73), residues: 57
  loop : -1.06 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 165 
 HIS   0.007   0.001   HIS B 374 
 PHE   0.018   0.002   PHE B 400 
 TYR   0.043   0.002   TYR B 381 
 ARG   0.003   0.000   ARG B 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00276 (    7)
  link_NAG-ASN         : angle       1.75380 (   21)
  link_BETA1-4         : bond        0.02246 (    1)
  link_BETA1-4         : angle       5.48893 (    3)
  hydrogen bonds       : bond        0.05195 (  289)
  hydrogen bonds       : angle       4.77372 (  831)
  SS BOND              : bond        0.00388 (    1)
  SS BOND              : angle       0.65161 (    2)
  covalent geometry    : bond        0.00506 ( 6748)
  covalent geometry    : angle       0.67966 ( 9171)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8867 (m-30) cc_final: 0.8375 (m-30)
REVERT: A  444 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7652 (mtpm)
REVERT: B   98 GLN cc_start: 0.7716 (tt0) cc_final: 0.7433 (tt0)
REVERT: B  227 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: B  383 MET cc_start: 0.8730 (mtp) cc_final: 0.8465 (mtp)
REVERT: B  479 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7540 (mt-10)
REVERT: B  571 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8102 (tt0)
REVERT: B  597 ASP cc_start: 0.7541 (m-30) cc_final: 0.7022 (t0)
  outliers start: 14
  outliers final: 6
  residues processed: 105
  average time/residue: 1.6221
  time to fit residues: 180.0900
Evaluate side-chains
  98 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  571 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 13 optimal weight:    0.2980
   chunk 48 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0670
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.0122

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
B  34 HIS
B 159 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.151455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.115054 restraints weight = 14481.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.95
r_work: 0.3144 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6757  Z= 0.177
  Angle     :  0.632   9.676   9197  Z= 0.304
  Chirality :  0.045   0.252    980
  Planarity :  0.004   0.052   1179
  Dihedral  :  9.892  76.251   1034
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 12.63 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.30), residues: 793
  helix:  0.67 (0.27), residues: 381
  sheet: -0.25 (0.73), residues: 57
  loop : -1.02 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 165 
 HIS   0.006   0.001   HIS B 374 
 PHE   0.011   0.001   PHE B 315 
 TYR   0.029   0.002   TYR B 381 
 ARG   0.005   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00342 (    7)
  link_NAG-ASN         : angle       1.87504 (   21)
  link_BETA1-4         : bond        0.01891 (    1)
  link_BETA1-4         : angle       4.73566 (    3)
  hydrogen bonds       : bond        0.04907 (  289)
  hydrogen bonds       : angle       4.63309 (  831)
  SS BOND              : bond        0.00285 (    1)
  SS BOND              : angle       0.72858 (    2)
  covalent geometry    : bond        0.00419 ( 6748)
  covalent geometry    : angle       0.62048 ( 9171)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8859 (m-30) cc_final: 0.8393 (m-30)
REVERT: A  444 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7680 (mtpm)
REVERT: B   63 ASN cc_start: 0.8047 (m110) cc_final: 0.7731 (m110)
REVERT: B   98 GLN cc_start: 0.7709 (tt0) cc_final: 0.7443 (tt0)
REVERT: B  227 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7872 (mt-10)
REVERT: B  383 MET cc_start: 0.8715 (mtp) cc_final: 0.8479 (mtp)
REVERT: B  479 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7477 (mt-10)
REVERT: B  571 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8068 (tt0)
REVERT: B  597 ASP cc_start: 0.7501 (m-30) cc_final: 0.6996 (t0)
  outliers start: 20
  outliers final: 11
  residues processed: 107
  average time/residue: 2.0203
  time to fit residues: 228.0204
Evaluate side-chains
  101 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 1.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  312 GLU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  571 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   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 474 GLN
B 159 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.151383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.113969 restraints weight = 21716.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 3.64
r_work: 0.3124 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6757  Z= 0.154
  Angle     :  0.601   9.700   9197  Z= 0.290
  Chirality :  0.044   0.263    980
  Planarity :  0.004   0.055   1179
  Dihedral  :  8.887  69.974   1034
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 13.92 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.30), residues: 793
  helix:  0.71 (0.27), residues: 381
  sheet: -0.26 (0.73), residues: 57
  loop : -0.97 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 165 
 HIS   0.006   0.001   HIS B 374 
 PHE   0.011   0.001   PHE B 327 
 TYR   0.023   0.002   TYR B 385 
 ARG   0.004   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00344 (    7)
  link_NAG-ASN         : angle       2.00550 (   21)
  link_BETA1-4         : bond        0.01698 (    1)
  link_BETA1-4         : angle       4.66697 (    3)
  hydrogen bonds       : bond        0.04659 (  289)
  hydrogen bonds       : angle       4.54766 (  831)
  SS BOND              : bond        0.00273 (    1)
  SS BOND              : angle       0.64984 (    2)
  covalent geometry    : bond        0.00362 ( 6748)
  covalent geometry    : angle       0.58813 ( 9171)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.838 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8887 (m-30) cc_final: 0.8414 (m-30)
REVERT: A  428 ASP cc_start: 0.8001 (p0) cc_final: 0.7737 (p0)
REVERT: A  444 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7656 (mtpm)
REVERT: B   63 ASN cc_start: 0.8081 (m110) cc_final: 0.7724 (m110)
REVERT: B   98 GLN cc_start: 0.7716 (tt0) cc_final: 0.7465 (tt0)
REVERT: B  227 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7914 (mt-10)
REVERT: B  479 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7515 (mt-10)
REVERT: B  571 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8109 (tt0)
REVERT: B  597 ASP cc_start: 0.7523 (m-30) cc_final: 0.6981 (t0)
  outliers start: 22
  outliers final: 14
  residues processed: 112
  average time/residue: 0.9856
  time to fit residues: 117.5284
Evaluate side-chains
  105 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  312 GLU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  571 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0170
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   overall best weight:    1.1220

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
B 159 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.150129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.112465 restraints weight = 24053.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 3.99
r_work: 0.3076 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3037
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3037
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6757  Z= 0.190
  Angle     :  0.631   9.723   9197  Z= 0.306
  Chirality :  0.045   0.264    980
  Planarity :  0.004   0.057   1179
  Dihedral  :  8.599  67.144   1034
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 14.63 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.30), residues: 793
  helix:  0.67 (0.27), residues: 381
  sheet: -0.31 (0.72), residues: 57
  loop : -0.96 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.006   0.001   HIS B 374 
 PHE   0.010   0.002   PHE B 315 
 TYR   0.022   0.002   TYR B 385 
 ARG   0.004   0.000   ARG B 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00311 (    7)
  link_NAG-ASN         : angle       1.96758 (   21)
  link_BETA1-4         : bond        0.01722 (    1)
  link_BETA1-4         : angle       4.68870 (    3)
  hydrogen bonds       : bond        0.04922 (  289)
  hydrogen bonds       : angle       4.58996 (  831)
  SS BOND              : bond        0.00276 (    1)
  SS BOND              : angle       0.71864 (    2)
  covalent geometry    : bond        0.00453 ( 6748)
  covalent geometry    : angle       0.61943 ( 9171)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8912 (m-30) cc_final: 0.8435 (m-30)
REVERT: A  428 ASP cc_start: 0.7926 (p0) cc_final: 0.7649 (p0)
REVERT: A  444 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7689 (mtpm)
REVERT: B   63 ASN cc_start: 0.8087 (m110) cc_final: 0.7724 (m110)
REVERT: B   98 GLN cc_start: 0.7680 (tt0) cc_final: 0.7439 (tt0)
REVERT: B  227 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7898 (mt-10)
REVERT: B  571 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8139 (tt0)
REVERT: B  597 ASP cc_start: 0.7526 (m-30) cc_final: 0.6962 (t0)
  outliers start: 25
  outliers final: 15
  residues processed: 109
  average time/residue: 1.0299
  time to fit residues: 119.1818
Evaluate side-chains
  106 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  257 SER
Chi-restraints excluded: chain B residue  261 CYS
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  571 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
B 159 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.148869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.112346 restraints weight = 17291.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 3.15
r_work: 0.3111 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3134
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3134
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6757  Z= 0.209
  Angle     :  0.643   9.733   9197  Z= 0.314
  Chirality :  0.045   0.262    980
  Planarity :  0.004   0.058   1179
  Dihedral  :  8.458  65.640   1034
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 14.92 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.30), residues: 793
  helix:  0.60 (0.27), residues: 386
  sheet: -0.38 (0.72), residues: 57
  loop : -0.92 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.006   0.001   HIS B 374 
 PHE   0.011   0.002   PHE B 327 
 TYR   0.020   0.002   TYR B 385 
 ARG   0.003   0.000   ARG B 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00308 (    7)
  link_NAG-ASN         : angle       1.99631 (   21)
  link_BETA1-4         : bond        0.01764 (    1)
  link_BETA1-4         : angle       4.78715 (    3)
  hydrogen bonds       : bond        0.05059 (  289)
  hydrogen bonds       : angle       4.63319 (  831)
  SS BOND              : bond        0.00298 (    1)
  SS BOND              : angle       0.66577 (    2)
  covalent geometry    : bond        0.00498 ( 6748)
  covalent geometry    : angle       0.63083 ( 9171)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A  354 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7605 (t0)
REVERT: A  420 ASP cc_start: 0.8887 (m-30) cc_final: 0.8401 (m-30)
REVERT: A  444 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7679 (mtpm)
REVERT: B   63 ASN cc_start: 0.8071 (m110) cc_final: 0.7726 (m110)
REVERT: B   98 GLN cc_start: 0.7780 (tt0) cc_final: 0.7513 (tt0)
REVERT: B  171 GLU cc_start: 0.7603 (tt0) cc_final: 0.7178 (tt0)
REVERT: B  227 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7909 (mt-10)
REVERT: B  571 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8137 (tt0)
REVERT: B  597 ASP cc_start: 0.7529 (m-30) cc_final: 0.6990 (t0)
  outliers start: 26
  outliers final: 13
  residues processed: 107
  average time/residue: 0.9908
  time to fit residues: 112.8023
Evaluate side-chains
  101 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  261 CYS
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  571 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0170
   chunk 67 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
B 159 ASN
B 522 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.152195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.115775 restraints weight = 14553.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 3.03
r_work: 0.3157 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3176
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6757  Z= 0.136
  Angle     :  0.596   9.685   9197  Z= 0.288
  Chirality :  0.043   0.252    980
  Planarity :  0.004   0.060   1179
  Dihedral  :  7.814  58.476   1034
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.07 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.31), residues: 793
  helix:  0.75 (0.27), residues: 385
  sheet: -0.34 (0.72), residues: 57
  loop : -0.87 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.006   0.001   HIS B  34 
 PHE   0.012   0.001   PHE B 327 
 TYR   0.019   0.001   TYR B 385 
 ARG   0.004   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00314 (    7)
  link_NAG-ASN         : angle       1.82540 (   21)
  link_BETA1-4         : bond        0.01737 (    1)
  link_BETA1-4         : angle       4.84518 (    3)
  hydrogen bonds       : bond        0.04479 (  289)
  hydrogen bonds       : angle       4.49735 (  831)
  SS BOND              : bond        0.00193 (    1)
  SS BOND              : angle       0.53801 (    2)
  covalent geometry    : bond        0.00315 ( 6748)
  covalent geometry    : angle       0.58364 ( 9171)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.720 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8839 (m-30) cc_final: 0.8532 (m-30)
REVERT: A  444 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7641 (mtpm)
REVERT: B   37 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6780 (mm-30)
REVERT: B   63 ASN cc_start: 0.8056 (m110) cc_final: 0.7699 (m110)
REVERT: B   98 GLN cc_start: 0.7619 (tt0) cc_final: 0.7416 (tt0)
REVERT: B  227 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7875 (mt-10)
REVERT: B  571 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8087 (tt0)
REVERT: B  597 ASP cc_start: 0.7469 (m-30) cc_final: 0.6957 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 111
  average time/residue: 1.0665
  time to fit residues: 125.8525
Evaluate side-chains
  106 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   37 GLU
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  261 CYS
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  571 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    0.0370
   chunk 68 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
A 506 GLN
B 159 ASN
B 522 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.151979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.114898 restraints weight = 18229.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 3.30
r_work: 0.3154 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6757  Z= 0.130
  Angle     :  0.580   9.662   9197  Z= 0.281
  Chirality :  0.043   0.248    980
  Planarity :  0.004   0.064   1179
  Dihedral  :  7.166  57.259   1034
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.36 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.31), residues: 793
  helix:  0.76 (0.27), residues: 388
  sheet: -0.28 (0.72), residues: 57
  loop : -0.82 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 165 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.012   0.001   PHE B 327 
 TYR   0.019   0.001   TYR B 385 
 ARG   0.003   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00333 (    7)
  link_NAG-ASN         : angle       1.71326 (   21)
  link_BETA1-4         : bond        0.01771 (    1)
  link_BETA1-4         : angle       5.17750 (    3)
  hydrogen bonds       : bond        0.04365 (  289)
  hydrogen bonds       : angle       4.43310 (  831)
  SS BOND              : bond        0.00224 (    1)
  SS BOND              : angle       0.57655 (    2)
  covalent geometry    : bond        0.00300 ( 6748)
  covalent geometry    : angle       0.56738 ( 9171)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.666 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8826 (m-30) cc_final: 0.8511 (m-30)
REVERT: A  444 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7672 (mtpm)
REVERT: A  471 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7240 (mm-30)
REVERT: B   63 ASN cc_start: 0.8066 (m110) cc_final: 0.7707 (m110)
REVERT: B   98 GLN cc_start: 0.7707 (tt0) cc_final: 0.7502 (tt0)
REVERT: B  227 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7902 (mt-10)
REVERT: B  597 ASP cc_start: 0.7456 (m-30) cc_final: 0.6956 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 104
  average time/residue: 1.0720
  time to fit residues: 119.1012
Evaluate side-chains
  105 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  261 CYS
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
A 506 GLN
B 159 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.152139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.114555 restraints weight = 18227.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 3.39
r_work: 0.3127 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3138
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3138
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6757  Z= 0.155
  Angle     :  0.603   9.689   9197  Z= 0.291
  Chirality :  0.043   0.248    980
  Planarity :  0.004   0.065   1179
  Dihedral  :  6.922  57.571   1034
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.93 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.31), residues: 793
  helix:  0.78 (0.27), residues: 386
  sheet: -0.30 (0.71), residues: 57
  loop : -0.88 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.006   0.001   HIS B 374 
 PHE   0.011   0.001   PHE A 338 
 TYR   0.019   0.002   TYR B 385 
 ARG   0.002   0.000   ARG B 460 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00330 (    7)
  link_NAG-ASN         : angle       1.63957 (   21)
  link_BETA1-4         : bond        0.01798 (    1)
  link_BETA1-4         : angle       5.36165 (    3)
  hydrogen bonds       : bond        0.04584 (  289)
  hydrogen bonds       : angle       4.47008 (  831)
  SS BOND              : bond        0.00257 (    1)
  SS BOND              : angle       0.63465 (    2)
  covalent geometry    : bond        0.00367 ( 6748)
  covalent geometry    : angle       0.59099 ( 9171)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8856 (m-30) cc_final: 0.8547 (m-30)
REVERT: A  444 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7728 (mtpm)
REVERT: B   63 ASN cc_start: 0.8071 (m110) cc_final: 0.7714 (m110)
REVERT: B  227 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7912 (mt-10)
REVERT: B  571 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8112 (tt0)
REVERT: B  597 ASP cc_start: 0.7477 (m-30) cc_final: 0.6960 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 104
  average time/residue: 0.9510
  time to fit residues: 105.7030
Evaluate side-chains
  103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  261 CYS
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  571 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    0.4980
   chunk 46 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0370
   chunk 5 optimal weight:    0.0770
   chunk 69 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.5016

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
B 159 ASN
B 522 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.151963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.114732 restraints weight = 18450.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 3.33
r_work: 0.3170 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3158
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6757  Z= 0.126
  Angle     :  0.579   9.658   9197  Z= 0.282
  Chirality :  0.042   0.248    980
  Planarity :  0.004   0.067   1179
  Dihedral  :  6.669  57.434   1034
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.36 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.31), residues: 793
  helix:  0.78 (0.27), residues: 388
  sheet: -0.28 (0.72), residues: 57
  loop : -0.85 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.012   0.001   PHE B 327 
 TYR   0.019   0.001   TYR B 385 
 ARG   0.003   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00330 (    7)
  link_NAG-ASN         : angle       1.53683 (   21)
  link_BETA1-4         : bond        0.01795 (    1)
  link_BETA1-4         : angle       5.39541 (    3)
  hydrogen bonds       : bond        0.04388 (  289)
  hydrogen bonds       : angle       4.42882 (  831)
  SS BOND              : bond        0.00210 (    1)
  SS BOND              : angle       0.56302 (    2)
  covalent geometry    : bond        0.00288 ( 6748)
  covalent geometry    : angle       0.56663 ( 9171)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.682 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8824 (m-30) cc_final: 0.8518 (m-30)
REVERT: A  444 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7730 (mtpm)
REVERT: A  471 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7227 (mm-30)
REVERT: B   63 ASN cc_start: 0.8079 (m110) cc_final: 0.7731 (m110)
REVERT: B  171 GLU cc_start: 0.7708 (tt0) cc_final: 0.7055 (pt0)
REVERT: B  227 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7909 (mt-10)
REVERT: B  571 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8092 (tt0)
REVERT: B  597 ASP cc_start: 0.7425 (m-30) cc_final: 0.6917 (t0)
  outliers start: 18
  outliers final: 14
  residues processed: 101
  average time/residue: 1.0333
  time to fit residues: 112.2093
Evaluate side-chains
  104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  261 CYS
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  571 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0470
   chunk 65 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0010
   chunk 14 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.5286

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
A 506 GLN
B 159 ASN
B 522 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.154010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.118630 restraints weight = 18155.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 3.30
r_work: 0.3175 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6757  Z= 0.124
  Angle     :  0.570   9.625   9197  Z= 0.276
  Chirality :  0.042   0.246    980
  Planarity :  0.004   0.067   1179
  Dihedral  :  6.171  57.162   1034
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.50 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.31), residues: 793
  helix:  0.80 (0.27), residues: 389
  sheet: -0.27 (0.72), residues: 57
  loop : -0.83 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.012   0.001   PHE A 338 
 TYR   0.019   0.001   TYR B 385 
 ARG   0.003   0.000   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00341 (    7)
  link_NAG-ASN         : angle       1.44596 (   21)
  link_BETA1-4         : bond        0.01807 (    1)
  link_BETA1-4         : angle       5.54320 (    3)
  hydrogen bonds       : bond        0.04262 (  289)
  hydrogen bonds       : angle       4.38270 (  831)
  SS BOND              : bond        0.00206 (    1)
  SS BOND              : angle       0.62782 (    2)
  covalent geometry    : bond        0.00286 ( 6748)
  covalent geometry    : angle       0.55737 ( 9171)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5680.21 seconds
wall clock time: 100 minutes 5.14 seconds (6005.14 seconds total)