Starting phenix.real_space_refine
on Fri Aug 22 17:41:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wgw_37517/08_2025/8wgw_37517.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wgw_37517/08_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_37517/08_2025/8wgw_37517.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wgw_37517/08_2025/8wgw_37517.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wgw_37517/08_2025/8wgw_37517.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wgw_37517/08_2025/8wgw_37517.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.005 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.74, per 1000 atoms: 0.27
  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: 0.49
  Conformation dependent library (CDL) restraints added in 370.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.13
  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: 0.85

  Time building geometry restraints manager: 0.69 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:             4.440
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.040
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.760
-------------------------------------------------------------------------------
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 : 8.88
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (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
 ARG   0.002   0.000   ARG A 357 
 TYR   0.022   0.001   TYR B 381 
 PHE   0.011   0.001   PHE B 369 
 TRP   0.009   0.001   TRP B 566 
 HIS   0.004   0.001   HIS B 374 

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

*********************** 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  : 0.260 
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: 0.8793 (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: 0.5479
  time to fit residues: 68.4587
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  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.0970
   overall best weight:    1.3582

-------------------------------------------------------------------------------
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 = 0.3710 r_free = 0.3710 target = 0.149356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.112452 restraints weight = 16835.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 3.18
r_work: 0.3129 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    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 = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6757  Z= 0.224
  Angle     :  0.689   9.386   9197  Z= 0.331
  Chirality :  0.048   0.267    980
  Planarity :  0.005   0.050   1179
  Dihedral  : 14.396  83.698   1034
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.33 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.30), residues: 793
  helix:  0.65 (0.27), residues: 383
  sheet: -0.13 (0.74), residues: 57
  loop : -1.05 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 460 
 TYR   0.041   0.002   TYR B 381 
 PHE   0.016   0.002   PHE B 400 
 TRP   0.011   0.001   TRP B 165 
 HIS   0.007   0.001   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 6748)
  covalent geometry    : angle       0.67825 ( 9171)
  SS BOND              : bond        0.00447 (    1)
  SS BOND              : angle       0.69100 (    2)
  hydrogen bonds       : bond        0.05282 (  289)
  hydrogen bonds       : angle       4.79912 (  831)
  link_BETA1-4         : bond        0.01959 (    1)
  link_BETA1-4         : angle       5.16345 (    3)
  link_NAG-ASN         : bond        0.00253 (    7)
  link_NAG-ASN         : angle       1.77452 (   21)

*********************** 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
  108 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8893 (m-30) cc_final: 0.8431 (m-30)
REVERT: A  444 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7675 (mtpm)
REVERT: B   98 GLN cc_start: 0.7765 (tt0) cc_final: 0.7505 (tt0)
REVERT: B  227 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7853 (mt-10)
REVERT: B  383 MET cc_start: 0.8756 (mtp) cc_final: 0.8483 (mtp)
REVERT: B  479 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7507 (mt-10)
REVERT: B  571 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8118 (tt0)
REVERT: B  597 ASP cc_start: 0.7553 (m-30) cc_final: 0.7036 (t0)
  outliers start: 13
  outliers final: 6
  residues processed: 104
  average time/residue: 0.5337
  time to fit residues: 58.5776
Evaluate side-chains
  97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
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 35 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0980
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
A 474 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 = 0.3752 r_free = 0.3752 target = 0.153262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.115962 restraints weight = 17820.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 3.26
r_work: 0.3174 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6757  Z= 0.132
  Angle     :  0.607   9.651   9197  Z= 0.289
  Chirality :  0.044   0.246    980
  Planarity :  0.004   0.051   1179
  Dihedral  : 10.112  76.317   1034
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 12.91 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.30), residues: 793
  helix:  0.82 (0.27), residues: 377
  sheet: -0.22 (0.73), residues: 57
  loop : -0.98 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 357 
 TYR   0.025   0.001   TYR B 385 
 PHE   0.011   0.001   PHE B 369 
 TRP   0.011   0.001   TRP B 165 
 HIS   0.007   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6748)
  covalent geometry    : angle       0.59594 ( 9171)
  SS BOND              : bond        0.00251 (    1)
  SS BOND              : angle       0.65915 (    2)
  hydrogen bonds       : bond        0.04545 (  289)
  hydrogen bonds       : angle       4.55174 (  831)
  link_BETA1-4         : bond        0.01902 (    1)
  link_BETA1-4         : angle       4.70311 (    3)
  link_NAG-ASN         : bond        0.00366 (    7)
  link_NAG-ASN         : angle       1.73213 (   21)

*********************** 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
  111 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8844 (m-30) cc_final: 0.8389 (m-30)
REVERT: A  444 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7656 (mtpm)
REVERT: B   63 ASN cc_start: 0.8048 (m110) cc_final: 0.7734 (m110)
REVERT: B   98 GLN cc_start: 0.7669 (tt0) cc_final: 0.7437 (tt0)
REVERT: B  227 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7895 (mt-10)
REVERT: B  383 MET cc_start: 0.8713 (mtp) cc_final: 0.8464 (mtp)
REVERT: B  479 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7476 (mt-10)
REVERT: B  597 ASP cc_start: 0.7465 (m-30) cc_final: 0.6946 (t0)
  outliers start: 18
  outliers final: 10
  residues processed: 103
  average time/residue: 0.4938
  time to fit residues: 53.8322
Evaluate side-chains
  99 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 ASN
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  266 LEU
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0170
   chunk 15 optimal weight:    0.1980
   chunk 68 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.5622

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
A 474 GLN
A 506 GLN
B 522 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.153613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.116396 restraints weight = 17864.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 3.26
r_work: 0.3179 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3167
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3167 r_free = 0.3167    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3167
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
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      :  0.003   0.043   6757  Z= 0.130
  Angle     :  0.583   9.679   9197  Z= 0.279
  Chirality :  0.043   0.255    980
  Planarity :  0.004   0.055   1179
  Dihedral  :  8.904  70.262   1034
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 13.63 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.31), residues: 793
  helix:  0.83 (0.27), residues: 381
  sheet: -0.16 (0.74), residues: 57
  loop : -0.96 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 357 
 TYR   0.023   0.001   TYR B 385 
 PHE   0.010   0.001   PHE B 369 
 TRP   0.011   0.001   TRP B 165 
 HIS   0.006   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6748)
  covalent geometry    : angle       0.57022 ( 9171)
  SS BOND              : bond        0.00249 (    1)
  SS BOND              : angle       0.56130 (    2)
  hydrogen bonds       : bond        0.04409 (  289)
  hydrogen bonds       : angle       4.45112 (  831)
  link_BETA1-4         : bond        0.01750 (    1)
  link_BETA1-4         : angle       4.67359 (    3)
  link_NAG-ASN         : bond        0.00364 (    7)
  link_NAG-ASN         : angle       1.87826 (   21)

*********************** 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
  119 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.8835 (m-30) cc_final: 0.8380 (m-30)
REVERT: A  444 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7641 (mtpm)
REVERT: B   63 ASN cc_start: 0.8066 (m110) cc_final: 0.7701 (m110)
REVERT: B   98 GLN cc_start: 0.7639 (tt0) cc_final: 0.7390 (tt0)
REVERT: B  227 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: B  383 MET cc_start: 0.8758 (mtp) cc_final: 0.8543 (mtp)
REVERT: B  479 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7435 (mt-10)
REVERT: B  597 ASP cc_start: 0.7447 (m-30) cc_final: 0.6936 (t0)
  outliers start: 21
  outliers final: 10
  residues processed: 109
  average time/residue: 0.5707
  time to fit residues: 65.9039
Evaluate side-chains
  101 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  121 ASN
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 3 optimal weight:    0.4980
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.152642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.116434 restraints weight = 14701.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 3.00
r_work: 0.3167 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3165
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3165
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6757  Z= 0.152
  Angle     :  0.602   9.657   9197  Z= 0.291
  Chirality :  0.044   0.265    980
  Planarity :  0.004   0.056   1179
  Dihedral  :  8.299  64.578   1034
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 15.21 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.30), residues: 793
  helix:  0.81 (0.27), residues: 381
  sheet: -0.17 (0.73), residues: 57
  loop : -0.96 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 346 
 TYR   0.023   0.002   TYR B 385 
 PHE   0.010   0.001   PHE B 315 
 TRP   0.010   0.001   TRP B 165 
 HIS   0.007   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6748)
  covalent geometry    : angle       0.58979 ( 9171)
  SS BOND              : bond        0.00271 (    1)
  SS BOND              : angle       0.61385 (    2)
  hydrogen bonds       : bond        0.04540 (  289)
  hydrogen bonds       : angle       4.43574 (  831)
  link_BETA1-4         : bond        0.01634 (    1)
  link_BETA1-4         : angle       4.64386 (    3)
  link_NAG-ASN         : bond        0.00337 (    7)
  link_NAG-ASN         : angle       1.88549 (   21)

*********************** 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
  119 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  354 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7501 (t0)
REVERT: A  420 ASP cc_start: 0.8843 (m-30) cc_final: 0.8516 (m-30)
REVERT: A  440 LYS cc_start: 0.8464 (mptt) cc_final: 0.8235 (mptm)
REVERT: A  444 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7660 (mtpm)
REVERT: B   63 ASN cc_start: 0.8077 (m110) cc_final: 0.7715 (m110)
REVERT: B   98 GLN cc_start: 0.7671 (tt0) cc_final: 0.7435 (tt0)
REVERT: B  227 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7878 (mt-10)
REVERT: B  383 MET cc_start: 0.8771 (mtp) cc_final: 0.8559 (mtp)
REVERT: B  597 ASP cc_start: 0.7466 (m-30) cc_final: 0.6940 (t0)
  outliers start: 21
  outliers final: 13
  residues processed: 109
  average time/residue: 0.5006
  time to fit residues: 57.8978
Evaluate side-chains
  102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  394 ASN
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  257 SER
Chi-restraints excluded: chain B residue  266 LEU
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3726 r_free = 0.3726 target = 0.151620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.115280 restraints weight = 23436.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 3.76
r_work: 0.3117 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3125
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.1556

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= 0.144
  Angle     :  0.590   9.654   9197  Z= 0.286
  Chirality :  0.044   0.253    980
  Planarity :  0.004   0.058   1179
  Dihedral  :  7.776  58.683   1034
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 15.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.31), residues: 793
  helix:  0.86 (0.28), residues: 380
  sheet: -0.22 (0.73), residues: 57
  loop : -0.93 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 346 
 TYR   0.021   0.002   TYR B 385 
 PHE   0.011   0.001   PHE B 315 
 TRP   0.010   0.001   TRP B 165 
 HIS   0.007   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6748)
  covalent geometry    : angle       0.57777 ( 9171)
  SS BOND              : bond        0.00266 (    1)
  SS BOND              : angle       0.65688 (    2)
  hydrogen bonds       : bond        0.04498 (  289)
  hydrogen bonds       : angle       4.39391 (  831)
  link_BETA1-4         : bond        0.01739 (    1)
  link_BETA1-4         : angle       4.82889 (    3)
  link_NAG-ASN         : bond        0.00309 (    7)
  link_NAG-ASN         : angle       1.84891 (   21)

*********************** 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
  115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8896 (m-30) cc_final: 0.8573 (m-30)
REVERT: A  444 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7753 (mtpm)
REVERT: B   63 ASN cc_start: 0.8141 (m110) cc_final: 0.7776 (m110)
REVERT: B   98 GLN cc_start: 0.7748 (tt0) cc_final: 0.7511 (tt0)
REVERT: B  227 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7969 (mt-10)
REVERT: B  597 ASP cc_start: 0.7514 (m-30) cc_final: 0.6981 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 105
  average time/residue: 0.4913
  time to fit residues: 54.9034
Evaluate side-chains
  102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 ASN
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  257 SER
Chi-restraints excluded: chain B residue  266 LEU
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.152627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.115154 restraints weight = 19043.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 3.43
r_work: 0.3148 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    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 = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6757  Z= 0.154
  Angle     :  0.605   9.663   9197  Z= 0.292
  Chirality :  0.044   0.251    980
  Planarity :  0.004   0.061   1179
  Dihedral  :  7.511  57.374   1034
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 15.64 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.31), residues: 793
  helix:  0.83 (0.27), residues: 381
  sheet: -0.22 (0.73), residues: 57
  loop : -0.92 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 346 
 TYR   0.021   0.002   TYR B 385 
 PHE   0.010   0.001   PHE B 315 
 TRP   0.010   0.001   TRP B 165 
 HIS   0.007   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6748)
  covalent geometry    : angle       0.59241 ( 9171)
  SS BOND              : bond        0.00264 (    1)
  SS BOND              : angle       0.70482 (    2)
  hydrogen bonds       : bond        0.04563 (  289)
  hydrogen bonds       : angle       4.43265 (  831)
  link_BETA1-4         : bond        0.01800 (    1)
  link_BETA1-4         : angle       5.04873 (    3)
  link_NAG-ASN         : bond        0.00321 (    7)
  link_NAG-ASN         : angle       1.76537 (   21)

*********************** 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
  117 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8864 (m-30) cc_final: 0.8571 (m-30)
REVERT: A  444 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7713 (mtpm)
REVERT: B   63 ASN cc_start: 0.8091 (m110) cc_final: 0.7715 (m110)
REVERT: B   98 GLN cc_start: 0.7671 (tt0) cc_final: 0.7451 (tt0)
REVERT: B  227 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7877 (mt-10)
REVERT: B  383 MET cc_start: 0.8970 (mtp) cc_final: 0.8713 (mtp)
REVERT: B  597 ASP cc_start: 0.7473 (m-30) cc_final: 0.6954 (t0)
  outliers start: 24
  outliers final: 13
  residues processed: 108
  average time/residue: 0.5110
  time to fit residues: 58.5951
Evaluate side-chains
  101 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 ASN
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  257 SER
Chi-restraints excluded: chain B residue  266 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0470
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.7278

-------------------------------------------------------------------------------
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 = 0.3728 r_free = 0.3728 target = 0.151742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.122257 restraints weight = 11952.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.33
r_work: 0.3188 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3147
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3147 r_free = 0.3147    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3146
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1643

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= 0.144
  Angle     :  0.590   9.653   9197  Z= 0.287
  Chirality :  0.043   0.248    980
  Planarity :  0.004   0.064   1179
  Dihedral  :  7.030  57.365   1034
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.36 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.31), residues: 793
  helix:  0.82 (0.27), residues: 382
  sheet: -0.27 (0.72), residues: 57
  loop : -0.89 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 346 
 TYR   0.020   0.001   TYR B 385 
 PHE   0.010   0.001   PHE B 327 
 TRP   0.010   0.001   TRP B 165 
 HIS   0.007   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6748)
  covalent geometry    : angle       0.57714 ( 9171)
  SS BOND              : bond        0.00226 (    1)
  SS BOND              : angle       0.66616 (    2)
  hydrogen bonds       : bond        0.04457 (  289)
  hydrogen bonds       : angle       4.40370 (  831)
  link_BETA1-4         : bond        0.01823 (    1)
  link_BETA1-4         : angle       5.21948 (    3)
  link_NAG-ASN         : bond        0.00322 (    7)
  link_NAG-ASN         : angle       1.75801 (   21)

*********************** 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
  113 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8832 (m-30) cc_final: 0.8539 (m-30)
REVERT: A  428 ASP cc_start: 0.7943 (p0) cc_final: 0.7670 (p0)
REVERT: A  444 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7763 (mtpm)
REVERT: B   63 ASN cc_start: 0.8087 (m110) cc_final: 0.7718 (m110)
REVERT: B   98 GLN cc_start: 0.7666 (tt0) cc_final: 0.7460 (tt0)
REVERT: B  227 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7845 (mt-10)
REVERT: B  597 ASP cc_start: 0.7411 (m-30) cc_final: 0.6902 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 106
  average time/residue: 0.4709
  time to fit residues: 53.1749
Evaluate side-chains
  103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 ASN
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  257 SER
Chi-restraints excluded: chain B residue  266 LEU
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 49 optimal weight:    0.2980
   chunk 36 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3712 r_free = 0.3712 target = 0.150203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.113236 restraints weight = 20091.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 3.69
r_work: 0.3107 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6757  Z= 0.172
  Angle     :  0.615   9.651   9197  Z= 0.300
  Chirality :  0.044   0.248    980
  Planarity :  0.004   0.065   1179
  Dihedral  :  6.834  57.795   1034
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.22 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.31), residues: 793
  helix:  0.83 (0.27), residues: 385
  sheet: -0.26 (0.72), residues: 57
  loop : -0.86 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 346 
 TYR   0.020   0.002   TYR B 385 
 PHE   0.010   0.001   PHE B 315 
 TRP   0.009   0.001   TRP B 165 
 HIS   0.007   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 6748)
  covalent geometry    : angle       0.60264 ( 9171)
  SS BOND              : bond        0.00277 (    1)
  SS BOND              : angle       0.82287 (    2)
  hydrogen bonds       : bond        0.04737 (  289)
  hydrogen bonds       : angle       4.48136 (  831)
  link_BETA1-4         : bond        0.01841 (    1)
  link_BETA1-4         : angle       5.39503 (    3)
  link_NAG-ASN         : bond        0.00322 (    7)
  link_NAG-ASN         : angle       1.66952 (   21)

*********************** 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
  105 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8860 (m-30) cc_final: 0.8562 (m-30)
REVERT: A  444 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7724 (mtpm)
REVERT: B   63 ASN cc_start: 0.8072 (m110) cc_final: 0.7697 (m110)
REVERT: B  150 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6335 (mp0)
REVERT: B  171 GLU cc_start: 0.7634 (tt0) cc_final: 0.6974 (pt0)
REVERT: B  227 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7909 (mt-10)
REVERT: B  597 ASP cc_start: 0.7444 (m-30) cc_final: 0.6907 (t0)
  outliers start: 17
  outliers final: 13
  residues processed: 98
  average time/residue: 0.5013
  time to fit residues: 52.1866
Evaluate side-chains
  101 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 ASN
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  150 GLU
Chi-restraints excluded: chain B residue  257 SER
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 52 optimal weight:    0.3980
   chunk 21 optimal weight:    0.6980
   chunk 14 optimal weight:    0.3980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.152241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.115272 restraints weight = 17245.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 3.22
r_work: 0.3177 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1727

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= 0.131
  Angle     :  0.575   9.659   9197  Z= 0.281
  Chirality :  0.042   0.249    980
  Planarity :  0.004   0.067   1179
  Dihedral  :  6.352  57.387   1034
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.65 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.31), residues: 793
  helix:  0.87 (0.27), residues: 382
  sheet: -0.27 (0.73), residues: 57
  loop : -0.91 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 346 
 TYR   0.019   0.001   TYR B 385 
 PHE   0.010   0.001   PHE B 327 
 TRP   0.010   0.001   TRP B 566 
 HIS   0.006   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6748)
  covalent geometry    : angle       0.56279 ( 9171)
  SS BOND              : bond        0.00199 (    1)
  SS BOND              : angle       0.67661 (    2)
  hydrogen bonds       : bond        0.04354 (  289)
  hydrogen bonds       : angle       4.39889 (  831)
  link_BETA1-4         : bond        0.01824 (    1)
  link_BETA1-4         : angle       5.48671 (    3)
  link_NAG-ASN         : bond        0.00326 (    7)
  link_NAG-ASN         : angle       1.51118 (   21)

********************** 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
  107 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8837 (m-30) cc_final: 0.8542 (m-30)
REVERT: A  428 ASP cc_start: 0.7945 (p0) cc_final: 0.7663 (p0)
REVERT: A  444 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7701 (mtpm)
REVERT: B   63 ASN cc_start: 0.8077 (m110) cc_final: 0.7716 (m110)
REVERT: B  227 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7843 (mt-10)
REVERT: B  597 ASP cc_start: 0.7322 (m-30) cc_final: 0.6883 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 101
  average time/residue: 0.4551
  time to fit residues: 48.9243
Evaluate side-chains
  99 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 ASN
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 66 optimal weight:    0.1980
   chunk 40 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.151581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.114422 restraints weight = 18199.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 3.29
r_work: 0.3162 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    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 = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1749

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= 0.143
  Angle     :  0.583   9.632   9197  Z= 0.285
  Chirality :  0.043   0.247    980
  Planarity :  0.004   0.066   1179
  Dihedral  :  6.080  57.389   1034
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.50 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.31), residues: 793
  helix:  0.83 (0.27), residues: 389
  sheet: -0.31 (0.73), residues: 57
  loop : -0.88 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 346 
 TYR   0.019   0.001   TYR B 385 
 PHE   0.012   0.001   PHE A 338 
 TRP   0.010   0.001   TRP B 165 
 HIS   0.006   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6748)
  covalent geometry    : angle       0.57074 ( 9171)
  SS BOND              : bond        0.00200 (    1)
  SS BOND              : angle       0.69720 (    2)
  hydrogen bonds       : bond        0.04462 (  289)
  hydrogen bonds       : angle       4.39266 (  831)
  link_BETA1-4         : bond        0.01934 (    1)
  link_BETA1-4         : angle       5.57449 (    3)
  link_NAG-ASN         : bond        0.00333 (    7)
  link_NAG-ASN         : angle       1.46458 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2488.11 seconds
wall clock time: 43 minutes 7.39 seconds (2587.39 seconds total)