Starting phenix.real_space_refine
on Wed Mar  4 03:22:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hxk_35079/03_2026/8hxk_35079.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hxk_35079/03_2026/8hxk_35079.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hxk_35079/03_2026/8hxk_35079.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hxk_35079/03_2026/8hxk_35079.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hxk_35079/03_2026/8hxk_35079.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hxk_35079/03_2026/8hxk_35079.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    6596      2.51       5
     N    1709      2.21       5
     O    1981      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10340
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4894
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4894
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 566}
    Chain: "B"
      Number of atoms: 5320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 676, 5320
          Classifications: {'peptide': 676}
          Link IDs: {'PTRANS': 34, 'TRANS': 641}
    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: "D"
      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: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      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
  Time building chain proxies: 2.29, per 1000 atoms: 0.22
  Number of scatterers: 10340
  At special positions: 0
  Unit cell: (81.62, 107.06, 156.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1981      8.00
     N    1709      7.00
     C    6596      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  16 " - pdb=" SG  CYS B 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 287 " - pdb=" SG  CYS B 297 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 332 " - pdb=" SG  CYS B 357 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 375 " - pdb=" SG  CYS B 428 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 387 " - pdb=" SG  CYS B 521 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 476 " - pdb=" SG  CYS B 484 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 534 " - pdb=" SG  CYS B 586 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 613 " - pdb=" SG  CYS B 645 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 658 " - pdb=" SG  CYS B 667 " 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 D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A 701 " - " ASN A 322 "
      " NAG A 702 " - " ASN A 432 "
      " NAG A 703 " - " ASN A 546 "
      " NAG A 704 " - " ASN A 329 "
      " NAG B1301 " - " ASN B 366 "
      " NAG C   1 " - " ASN A  53 "
      " NAG D   1 " - " ASN B 339 "
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 522.6 milliseconds
  

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2386

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 14 sheets defined
      33.2% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.715A  pdb=" N   ARG A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 79
      removed outlier: 4.244A  pdb=" N   GLN A  60 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   TRP A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 109 through 128
    Processing helix  chain 'A' and resid 158 through 193
      removed outlier: 5.429A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.650A  pdb=" N   ALA A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 218 through 232
      removed outlier: 4.194A  pdb=" N   GLU A 232 " --> pdb=" O   ARG A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 4.255A  pdb=" N   ASP A 250 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   THR A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.548A  pdb=" N   ARG A 273 " --> pdb=" O   MET A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 324 through 330
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 4.298A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 448
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 481
      removed outlier: 3.631A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
      removed outlier: 4.084A  pdb=" N   SER A 502 " --> pdb=" O   ASP A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 532
      removed outlier: 3.994A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLN A 524 " --> pdb=" O   ILE A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 561
      removed outlier: 4.121A  pdb=" N   GLY A 561 " --> pdb=" O   MET A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
    Processing helix  chain 'A' and resid 581 through 597
      removed outlier: 3.592A  pdb=" N   LEU A 585 " --> pdb=" O   VAL A 581 " (cutoff:3.500A)
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'B' and resid 290 through 300
    Processing helix  chain 'B' and resid 334 through 339
    Processing helix  chain 'B' and resid 399 through 406
    Processing helix  chain 'B' and resid 498 through 502
    Processing helix  chain 'B' and resid 612 through 616
    Processing helix  chain 'B' and resid 627 through 632
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132
      removed outlier: 3.822A  pdb=" N   VAL A 132 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   PHE A 142 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.486A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 31
      removed outlier: 8.188A  pdb=" N   ASN B  62 " --> pdb=" O   TYR B 265 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   TYR B 265 " --> pdb=" O   ASN B  62 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   TYR B 203 " --> pdb=" O   VAL B 192 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 56
      removed outlier: 3.836A  pdb=" N   VAL B 285 " --> pdb=" O   MET B 272 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85
      removed outlier: 3.984A  pdb=" N   LEU B  84 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 129
    Processing sheet with id=AA8, first strand: chain 'B' and resid 195 through 196
    Processing sheet with id=AA9, first strand: chain 'B' and resid 321 through 323
      removed outlier: 8.156A  pdb=" N   ILE B 322 " --> pdb=" O   ASN B 538 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLU B 579 " --> pdb=" O   ASP B 574 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 357 through 358
      removed outlier: 6.828A  pdb=" N   CYS B 357 " --> pdb=" O   CYS B 521 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 390 through 392
    Processing sheet with id=AB3, first strand: chain 'B' and resid 395 through 398
    Processing sheet with id=AB4, first strand: chain 'B' and resid 448 through 450
    Processing sheet with id=AB5, first strand: chain 'B' and resid 607 through 609
      removed outlier: 6.687A  pdb=" N   CYS B 645 " --> pdb=" O   TYR B 608 " (cutoff:3.500A)

    336 hydrogen bonds defined for protein.
    951 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.21

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3263
        1.34 -     1.46: 2704
        1.46 -     1.59: 4574
        1.59 -     1.71: 0
        1.71 -     1.83: 80
  Bond restraints: 10621
  Sorted by residual:
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.489 -0.083 2.00e-02 2.50e+03 1.73e+01
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.460 -0.054 2.00e-02 2.50e+03 7.21e+00
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.460 -0.054 2.00e-02 2.50e+03 7.18e+00
  bond pdb=" CB  ASP B  85 "
       pdb=" CG  ASP B  85 "
    ideal  model  delta    sigma   weight residual
    1.516  1.562 -0.046 2.50e-02 1.60e+03 3.45e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.442 -0.036 2.00e-02 2.50e+03 3.20e+00
  ... (remaining 10616 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.98: 14156
        2.98 -     5.96: 235
        5.96 -     8.94: 44
        8.94 -    11.92: 9
       11.92 -    14.90: 3
  Bond angle restraints: 14447
  Sorted by residual:
  angle pdb=" O   GLY A  66 "
        pdb=" C   GLY A  66 "
        pdb=" N   ALA A  67 "
      ideal   model   delta    sigma   weight residual
     121.85  124.86   -3.01 5.60e-01 3.19e+00 2.88e+01
  angle pdb=" N   GLY A  66 "
        pdb=" CA  GLY A  66 "
        pdb=" C   GLY A  66 "
      ideal   model   delta    sigma   weight residual
     110.21  105.50    4.71 9.10e-01 1.21e+00 2.68e+01
  angle pdb=" CB  MET A 557 "
        pdb=" CG  MET A 557 "
        pdb=" SD  MET A 557 "
      ideal   model   delta    sigma   weight residual
     112.70  127.30  -14.60 3.00e+00 1.11e-01 2.37e+01
  angle pdb=" CA  LEU A 450 "
        pdb=" CB  LEU A 450 "
        pdb=" CG  LEU A 450 "
      ideal   model   delta    sigma   weight residual
     116.30  131.20  -14.90 3.50e+00 8.16e-02 1.81e+01
  angle pdb=" N   GLN A 556 "
        pdb=" CA  GLN A 556 "
        pdb=" CB  GLN A 556 "
      ideal   model   delta    sigma   weight residual
     110.28  116.78   -6.50 1.55e+00 4.16e-01 1.76e+01
  ... (remaining 14442 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 5683
       17.74 -    35.48: 571
       35.48 -    53.22: 119
       53.22 -    70.96: 13
       70.96 -    88.71: 12
  Dihedral angle restraints: 6398
    sinusoidal: 2670
      harmonic: 3728
  Sorted by residual:
  dihedral pdb=" CB  CYS B 534 "
           pdb=" SG  CYS B 534 "
           pdb=" SG  CYS B 586 "
           pdb=" CB  CYS B 586 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -5.22  -80.78     1      1.00e+01 1.00e-02 8.06e+01
  dihedral pdb=" CA  CYS B 387 "
           pdb=" C   CYS B 387 "
           pdb=" N   PHE B 388 "
           pdb=" CA  PHE B 388 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -143.91  -36.09     0      5.00e+00 4.00e-02 5.21e+01
  dihedral pdb=" CB  CYS B 658 "
           pdb=" SG  CYS B 658 "
           pdb=" SG  CYS B 667 "
           pdb=" CB  CYS B 667 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -135.08   49.08     1      1.00e+01 1.00e-02 3.31e+01
  ... (remaining 6395 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.117: 1485
       0.117 -    0.234: 80
       0.234 -    0.351: 7
       0.351 -    0.468: 0
       0.468 -    0.585: 1
  Chirality restraints: 1573
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A  53 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.82   -0.58 2.00e-01 2.50e+01 8.55e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN B 339 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" C1  NAG B1301 "
            pdb=" ND2 ASN B 366 "
            pdb=" C2  NAG B1301 "
            pdb=" O5  NAG B1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.47e+00
  ... (remaining 1570 not shown)

  Planarity restraints: 1863
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 444 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.21e+00
        pdb=" C   LEU A 444 "    0.046 2.00e-02 2.50e+03
        pdb=" O   LEU A 444 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASN A 445 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 388 "    0.017 2.00e-02 2.50e+03   1.94e-02 6.59e+00
        pdb=" CG  PHE B 388 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 388 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 388 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 388 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 388 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 388 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 582 "    0.040 5.00e-02 4.00e+02   6.08e-02 5.91e+00
        pdb=" N   PRO A 583 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1860 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 429
        2.71 -     3.26: 10927
        3.26 -     3.80: 18841
        3.80 -     4.35: 23214
        4.35 -     4.90: 36815
  Nonbonded interactions: 90226
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 286 "
            pdb=" OG  SER B 293 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OH  TYR B 203 "
            pdb=" OE2 GLU B 227 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OE2 GLU B 294 "
            pdb=" OG  SER B 312 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" NH2 ARG B 315 "
            pdb=" O   PHE B 588 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   VAL A 560 "
            pdb=" OG  SER A 563 "
     model   vdw
     2.286 3.040
  ... (remaining 90221 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.000
  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:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.950
  Find NCS groups from input model:        0.070
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5073
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      :  0.005   0.083  10643  Z= 0.233
  Angle     :  1.035  21.385  14500  Z= 0.520
  Chirality :  0.062   0.585   1573
  Planarity :  0.007   0.061   1856
  Dihedral  : 14.606  88.705   3973
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -2.65 (0.21), residues: 1269
  helix: -1.15 (0.24), residues: 400
  sheet: -1.87 (0.54), residues: 74
  loop : -2.18 (0.20), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 460 
 TYR   0.029   0.003   TYR B  67 
 PHE   0.044   0.003   PHE B 388 
 TRP   0.025   0.002   TRP A 610 
 HIS   0.016   0.002   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 (10621)
  covalent geometry    : angle       0.99558 (14447)
  SS BOND              : bond        0.00588 (   13)
  SS BOND              : angle       1.49857 (   26)
  hydrogen bonds       : bond        0.12739 (  336)
  hydrogen bonds       : angle       7.43939 (  951)
  link_BETA1-4         : bond        0.04199 (    2)
  link_BETA1-4         : angle       9.95397 (    6)
  link_NAG-ASN         : bond        0.01037 (    7)
  link_NAG-ASN         : angle       5.20518 (   21)

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

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

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 GLU cc_start: 0.7882 (pp20) cc_final: 0.7473 (pp20)
REVERT: A   34 HIS cc_start: 0.5397 (m90) cc_final: 0.4889 (m90)
REVERT: A  179 LEU cc_start: 0.7561 (tt) cc_final: 0.7208 (mp)
REVERT: A  180 TYR cc_start: 0.6582 (t80) cc_final: 0.6247 (t80)
REVERT: A  270 MET cc_start: 0.2534 (tpt) cc_final: 0.2236 (tpt)
REVERT: B  615 GLU cc_start: 0.7785 (mp0) cc_final: 0.7479 (mp0)
REVERT: B  656 TYR cc_start: 0.6479 (t80) cc_final: 0.6275 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1023
  time to fit residues: 32.3946
Evaluate side-chains
  134 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 123 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  26 GLN
B 122 ASN
B 350 ASN
B 552 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.126398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.105964 restraints weight = 59764.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.108850 restraints weight = 34256.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.110642 restraints weight = 22553.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.111792 restraints weight = 16464.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.112524 restraints weight = 13042.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.4417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6208
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  10643  Z= 0.222
  Angle     :  0.840  16.764  14500  Z= 0.428
  Chirality :  0.053   0.536   1573
  Planarity :  0.006   0.093   1856
  Dihedral  :  6.967  59.899   1583
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 20.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 10.93 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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 are not related in a simple way.
  whole: -2.47 (0.22), residues: 1269
  helix: -0.77 (0.25), residues: 409
  sheet: -2.29 (0.48), residues: 98
  loop : -2.12 (0.22), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 169 
 TYR   0.023   0.002   TYR B 491 
 PHE   0.047   0.003   PHE A 512 
 TRP   0.046   0.003   TRP A 461 
 HIS   0.014   0.002   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (10621)
  covalent geometry    : angle       0.80594 (14447)
  SS BOND              : bond        0.00432 (   13)
  SS BOND              : angle       1.83263 (   26)
  hydrogen bonds       : bond        0.05313 (  336)
  hydrogen bonds       : angle       6.30692 (  951)
  link_BETA1-4         : bond        0.02636 (    2)
  link_BETA1-4         : angle       7.57126 (    6)
  link_NAG-ASN         : bond        0.00893 (    7)
  link_NAG-ASN         : angle       4.46879 (   21)

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

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

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8537 (mp0)
REVERT: A  152 MET cc_start: 0.4282 (mmt) cc_final: 0.3223 (mmt)
REVERT: A  180 TYR cc_start: 0.7531 (t80) cc_final: 0.7235 (t80)
REVERT: A  270 MET cc_start: 0.3344 (tpt) cc_final: 0.2706 (tpt)
REVERT: A  476 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7518 (tttm)
REVERT: B  425 PHE cc_start: 0.7620 (t80) cc_final: 0.7305 (t80)
REVERT: B  656 TYR cc_start: 0.6980 (t80) cc_final: 0.6696 (t80)
  outliers start: 20
  outliers final: 11
  residues processed: 155
  average time/residue: 0.0994
  time to fit residues: 22.0565
Evaluate side-chains
  119 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  505 HIS
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  674 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 12 optimal weight:    0.0060
   chunk 82 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 68 optimal weight:   20.0000
   chunk 101 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   overall best weight:    1.3402

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 195 HIS
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4694 r_free = 0.4694 target = 0.124591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.104057 restraints weight = 58229.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.106941 restraints weight = 32967.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.108770 restraints weight = 21420.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.109918 restraints weight = 15470.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.110609 restraints weight = 12210.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.4386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6314
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10643  Z= 0.155
  Angle     :  0.740  16.952  14500  Z= 0.368
  Chirality :  0.050   0.468   1573
  Planarity :  0.006   0.071   1856
  Dihedral  :  6.573  57.766   1583
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 18.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.93 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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 are not related in a simple way.
  whole: -2.23 (0.23), residues: 1269
  helix: -0.46 (0.25), residues: 409
  sheet: -2.23 (0.49), residues: 94
  loop : -2.05 (0.22), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 245 
 TYR   0.022   0.002   TYR A 199 
 PHE   0.022   0.002   PHE A 464 
 TRP   0.062   0.003   TRP A 461 
 HIS   0.012   0.002   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10621)
  covalent geometry    : angle       0.70399 (14447)
  SS BOND              : bond        0.00328 (   13)
  SS BOND              : angle       1.20218 (   26)
  hydrogen bonds       : bond        0.04602 (  336)
  hydrogen bonds       : angle       6.01135 (  951)
  link_BETA1-4         : bond        0.02939 (    2)
  link_BETA1-4         : angle       7.69689 (    6)
  link_NAG-ASN         : bond        0.00800 (    7)
  link_NAG-ASN         : angle       4.29195 (   21)

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

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

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.4692 (mmt) cc_final: 0.3441 (mmt)
REVERT: A  180 TYR cc_start: 0.7545 (t80) cc_final: 0.7207 (t80)
REVERT: A  270 MET cc_start: 0.3765 (tpt) cc_final: 0.2998 (tpt)
REVERT: A  476 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7839 (tttm)
REVERT: B  398 VAL cc_start: 0.7113 (OUTLIER) cc_final: 0.6897 (m)
  outliers start: 28
  outliers final: 16
  residues processed: 152
  average time/residue: 0.0961
  time to fit residues: 21.0949
Evaluate side-chains
  122 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  505 HIS
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  534 CYS
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  556 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 122 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 119 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0370
   chunk 73 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.7864

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.123177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.101909 restraints weight = 51736.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.104919 restraints weight = 30396.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.106985 restraints weight = 20308.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.108326 restraints weight = 14860.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 62)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.109115 restraints weight = 11726.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.4382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6332
moved from start:          0.4731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10643  Z= 0.139
  Angle     :  0.734  16.465  14500  Z= 0.365
  Chirality :  0.050   0.471   1573
  Planarity :  0.005   0.057   1856
  Dihedral  :  6.339  55.901   1583
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 18.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.16 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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 are not related in a simple way.
  whole: -2.18 (0.23), residues: 1269
  helix: -0.38 (0.26), residues: 411
  sheet: -2.22 (0.52), residues: 80
  loop : -2.06 (0.21), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 404 
 TYR   0.022   0.001   TYR A  50 
 PHE   0.034   0.002   PHE B 425 
 TRP   0.038   0.002   TRP A 461 
 HIS   0.008   0.002   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10621)
  covalent geometry    : angle       0.70133 (14447)
  SS BOND              : bond        0.00363 (   13)
  SS BOND              : angle       1.12884 (   26)
  hydrogen bonds       : bond        0.04391 (  336)
  hydrogen bonds       : angle       5.82037 (  951)
  link_BETA1-4         : bond        0.02980 (    2)
  link_BETA1-4         : angle       7.42817 (    6)
  link_NAG-ASN         : bond        0.00796 (    7)
  link_NAG-ASN         : angle       4.09642 (   21)

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

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

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.4652 (mmt) cc_final: 0.3442 (mmt)
REVERT: A  180 TYR cc_start: 0.7685 (t80) cc_final: 0.7338 (t80)
REVERT: A  270 MET cc_start: 0.3689 (tpt) cc_final: 0.2698 (tpt)
REVERT: A  408 MET cc_start: 0.6403 (tmm) cc_final: 0.6099 (tmt)
REVERT: A  461 TRP cc_start: 0.8051 (m-10) cc_final: 0.7789 (m-90)
REVERT: A  474 MET cc_start: 0.6048 (ppp) cc_final: 0.5471 (mmm)
REVERT: A  476 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8191 (tttm)
REVERT: B  129 LYS cc_start: 0.3560 (OUTLIER) cc_final: 0.3336 (mtmm)
REVERT: B  398 VAL cc_start: 0.6820 (OUTLIER) cc_final: 0.6538 (m)
REVERT: B  615 GLU cc_start: 0.7721 (mp0) cc_final: 0.7393 (mp0)
  outliers start: 28
  outliers final: 18
  residues processed: 142
  average time/residue: 0.0873
  time to fit residues: 18.5964
Evaluate side-chains
  131 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  505 HIS
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  476 CYS
Chi-restraints excluded: chain B residue  534 CYS
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  674 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 120 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0870
   chunk 68 optimal weight:   20.0000
   chunk 56 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 115 optimal weight:    0.5980
   chunk 110 optimal weight:    0.0770
   overall best weight:    0.9520

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 195 HIS
A 596 GLN
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.120739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.098625 restraints weight = 54102.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.101479 restraints weight = 32364.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.103417 restraints weight = 22029.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.104691 restraints weight = 16536.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.105459 restraints weight = 13341.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.4315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6488
moved from start:          0.5164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10643  Z= 0.138
  Angle     :  0.708  15.814  14500  Z= 0.353
  Chirality :  0.049   0.461   1573
  Planarity :  0.005   0.056   1856
  Dihedral  :  6.174  55.687   1583
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 18.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.78 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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 are not related in a simple way.
  whole: -2.14 (0.23), residues: 1269
  helix: -0.35 (0.25), residues: 412
  sheet: -2.14 (0.53), residues: 80
  loop : -2.04 (0.21), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 245 
 TYR   0.016   0.001   TYR A 199 
 PHE   0.018   0.001   PHE B 338 
 TRP   0.031   0.002   TRP A 461 
 HIS   0.009   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10621)
  covalent geometry    : angle       0.67529 (14447)
  SS BOND              : bond        0.00288 (   13)
  SS BOND              : angle       1.05741 (   26)
  hydrogen bonds       : bond        0.04323 (  336)
  hydrogen bonds       : angle       5.74264 (  951)
  link_BETA1-4         : bond        0.03026 (    2)
  link_BETA1-4         : angle       7.15619 (    6)
  link_NAG-ASN         : bond        0.00760 (    7)
  link_NAG-ASN         : angle       3.99896 (   21)

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

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

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 120
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8642 (tt)
REVERT: A   98 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8143 (mm-40)
REVERT: A  152 MET cc_start: 0.4649 (mmt) cc_final: 0.3353 (mmt)
REVERT: A  180 TYR cc_start: 0.8096 (t80) cc_final: 0.7695 (t80)
REVERT: A  270 MET cc_start: 0.3711 (tpt) cc_final: 0.2656 (tpt)
REVERT: A  332 MET cc_start: 0.6407 (tpt) cc_final: 0.6187 (tpt)
REVERT: A  355 ASP cc_start: 0.6552 (t0) cc_final: 0.6333 (t0)
REVERT: A  408 MET cc_start: 0.6667 (tmm) cc_final: 0.6397 (tmt)
REVERT: A  421 MET cc_start: 0.6612 (ppp) cc_final: 0.6335 (ppp)
REVERT: A  474 MET cc_start: 0.5901 (ppp) cc_final: 0.5539 (mmm)
REVERT: A  476 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8400 (tttp)
REVERT: B  132 ASN cc_start: 0.3369 (OUTLIER) cc_final: 0.3079 (m110)
REVERT: B  398 VAL cc_start: 0.7056 (OUTLIER) cc_final: 0.6806 (m)
REVERT: B  615 GLU cc_start: 0.7705 (mp0) cc_final: 0.7461 (mp0)
  outliers start: 32
  outliers final: 16
  residues processed: 144
  average time/residue: 0.0807
  time to fit residues: 17.6175
Evaluate side-chains
  123 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  505 HIS
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  476 CYS
Chi-restraints excluded: chain B residue  534 CYS
Chi-restraints excluded: chain B residue  674 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 62 optimal weight:   20.0000
   chunk 116 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 92 optimal weight:    3.9990
   chunk 16 optimal weight:    8.9990
   chunk 41 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 442 GLN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 ASN
** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 502 GLN
B 538 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.104941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.083749 restraints weight = 59079.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.086715 restraints weight = 37614.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.087993 restraints weight = 21491.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.088302 restraints weight = 17489.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.088474 restraints weight = 14117.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.8305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.177  10643  Z= 0.331
  Angle     :  1.015  16.804  14500  Z= 0.527
  Chirality :  0.060   0.520   1573
  Planarity :  0.008   0.082   1856
  Dihedral  :  7.398  53.772   1583
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 32.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.21 %
    Favored  : 87.79 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.38 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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 are not related in a simple way.
  whole: -2.75 (0.21), residues: 1269
  helix: -0.95 (0.24), residues: 408
  sheet: -2.98 (0.62), residues: 44
  loop : -2.35 (0.20), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 169 
 TYR   0.034   0.004   TYR B 449 
 PHE   0.031   0.003   PHE B 237 
 TRP   0.022   0.003   TRP A 606 
 HIS   0.009   0.002   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00733 (10621)
  covalent geometry    : angle       0.98893 (14447)
  SS BOND              : bond        0.01213 (   13)
  SS BOND              : angle       1.51597 (   26)
  hydrogen bonds       : bond        0.06724 (  336)
  hydrogen bonds       : angle       6.61638 (  951)
  link_BETA1-4         : bond        0.02895 (    2)
  link_BETA1-4         : angle       7.51829 (    6)
  link_NAG-ASN         : bond        0.00785 (    7)
  link_NAG-ASN         : angle       4.40485 (   21)

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

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

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 115
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8935 (tt)
REVERT: A  176 LEU cc_start: 0.8217 (mt) cc_final: 0.7688 (mt)
REVERT: A  402 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7778 (tp30)
REVERT: A  455 MET cc_start: 0.8118 (ppp) cc_final: 0.7712 (ppp)
REVERT: A  467 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6383 (pm20)
REVERT: B  132 ASN cc_start: 0.3704 (OUTLIER) cc_final: 0.2959 (m-40)
REVERT: B  325 PHE cc_start: 0.3516 (m-80) cc_final: 0.2270 (m-80)
REVERT: B  342 THR cc_start: 0.7024 (m) cc_final: 0.6823 (m)
REVERT: B  508 VAL cc_start: 0.8211 (t) cc_final: 0.7916 (p)
  outliers start: 39
  outliers final: 24
  residues processed: 147
  average time/residue: 0.0890
  time to fit residues: 19.3048
Evaluate side-chains
  124 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  402 GLU
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  505 HIS
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  237 PHE
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  476 CYS
Chi-restraints excluded: chain B residue  534 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9990
   chunk 90 optimal weight:   40.0000
   chunk 12 optimal weight:    0.0870
   chunk 35 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 48 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    0.9964

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

Flipped N/Q/H residues before XYZ refinement:
A 524 GLN
A 534 GLN
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 ASN
** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 538 ASN
** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.108635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.087460 restraints weight = 54449.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.088978 restraints weight = 36521.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.091533 restraints weight = 23781.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.091349 restraints weight = 18098.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.091594 restraints weight = 14975.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.8411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  10643  Z= 0.153
  Angle     :  0.789  16.473  14500  Z= 0.390
  Chirality :  0.051   0.439   1573
  Planarity :  0.006   0.066   1856
  Dihedral  :  6.879  57.045   1583
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 19.42
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.98 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 22.13 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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 are not related in a simple way.
  whole: -2.40 (0.22), residues: 1269
  helix: -0.53 (0.25), residues: 412
  sheet: -2.62 (0.61), residues: 51
  loop : -2.22 (0.20), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 169 
 TYR   0.029   0.002   TYR A  50 
 PHE   0.025   0.002   PHE B 338 
 TRP   0.021   0.002   TRP A 461 
 HIS   0.010   0.002   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (10621)
  covalent geometry    : angle       0.75862 (14447)
  SS BOND              : bond        0.00397 (   13)
  SS BOND              : angle       1.12124 (   26)
  hydrogen bonds       : bond        0.04870 (  336)
  hydrogen bonds       : angle       5.75034 (  951)
  link_BETA1-4         : bond        0.03057 (    2)
  link_BETA1-4         : angle       7.37118 (    6)
  link_NAG-ASN         : bond        0.00782 (    7)
  link_NAG-ASN         : angle       4.14946 (   21)

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

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

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8610 (tt)
REVERT: A  176 LEU cc_start: 0.8002 (mt) cc_final: 0.7560 (mt)
REVERT: A  355 ASP cc_start: 0.6827 (t0) cc_final: 0.6584 (t0)
REVERT: A  360 MET cc_start: 0.8143 (pmm) cc_final: 0.7727 (pmm)
REVERT: B   60 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.6568 (t80)
REVERT: B  191 PHE cc_start: 0.0556 (OUTLIER) cc_final: 0.0318 (p90)
REVERT: B  325 PHE cc_start: 0.2864 (m-80) cc_final: 0.1844 (m-80)
REVERT: B  508 VAL cc_start: 0.8384 (t) cc_final: 0.8159 (p)
  outliers start: 29
  outliers final: 17
  residues processed: 130
  average time/residue: 0.0948
  time to fit residues: 17.8242
Evaluate side-chains
  112 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  505 HIS
Chi-restraints excluded: chain B residue   60 TYR
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue  191 PHE
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  476 CYS
Chi-restraints excluded: chain B residue  534 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0870
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 61 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0030
   chunk 114 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    0.5772

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

Flipped N/Q/H residues before XYZ refinement:
A 137 ASN
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 210 ASN
** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.108735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.087094 restraints weight = 54861.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.089580 restraints weight = 32025.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.090664 restraints weight = 21580.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.092109 restraints weight = 17299.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.092910 restraints weight = 13845.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
moved from start:          0.8502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10643  Z= 0.142
  Angle     :  0.772  16.183  14500  Z= 0.380
  Chirality :  0.050   0.440   1573
  Planarity :  0.005   0.058   1856
  Dihedral  :  6.596  57.477   1583
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 18.28
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.22 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 22.76 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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 are not related in a simple way.
  whole: -2.24 (0.22), residues: 1269
  helix: -0.39 (0.25), residues: 409
  sheet: -2.52 (0.66), residues: 51
  loop : -2.12 (0.21), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 563 
 TYR   0.025   0.002   TYR A  50 
 PHE   0.021   0.002   PHE B 338 
 TRP   0.014   0.001   TRP A 461 
 HIS   0.009   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (10621)
  covalent geometry    : angle       0.74188 (14447)
  SS BOND              : bond        0.00313 (   13)
  SS BOND              : angle       1.03186 (   26)
  hydrogen bonds       : bond        0.04683 (  336)
  hydrogen bonds       : angle       5.58030 (  951)
  link_BETA1-4         : bond        0.02875 (    2)
  link_BETA1-4         : angle       7.19905 (    6)
  link_NAG-ASN         : bond        0.00824 (    7)
  link_NAG-ASN         : angle       4.03064 (   21)

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

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

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8590 (tt)
REVERT: A  176 LEU cc_start: 0.7915 (mt) cc_final: 0.7533 (mt)
REVERT: A  323 MET cc_start: 0.6675 (ptm) cc_final: 0.6075 (ppp)
REVERT: A  355 ASP cc_start: 0.6614 (t0) cc_final: 0.6404 (t0)
REVERT: A  358 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8563 (mm)
REVERT: A  360 MET cc_start: 0.8252 (pmm) cc_final: 0.7910 (pmm)
REVERT: A  436 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.7056 (mm)
REVERT: A  446 ILE cc_start: 0.8740 (tt) cc_final: 0.8180 (pt)
REVERT: A  583 PRO cc_start: 0.8293 (Cg_exo) cc_final: 0.8086 (Cg_endo)
REVERT: B   60 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.6513 (t80)
REVERT: B  132 ASN cc_start: 0.3396 (OUTLIER) cc_final: 0.2922 (m-40)
REVERT: B  325 PHE cc_start: 0.2921 (m-80) cc_final: 0.1892 (m-80)
REVERT: B  656 TYR cc_start: 0.6867 (t80) cc_final: 0.6660 (t80)
  outliers start: 27
  outliers final: 15
  residues processed: 130
  average time/residue: 0.0891
  time to fit residues: 17.0474
Evaluate side-chains
  114 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain B residue   60 TYR
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  476 CYS
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  534 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 111 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 114 optimal weight:   20.0000
   chunk 44 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 110 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 113 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 ASN
B 210 ASN
** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.106417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.084994 restraints weight = 55410.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.087515 restraints weight = 31783.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.089148 restraints weight = 21639.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 63)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.090138 restraints weight = 16246.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.090845 restraints weight = 13297.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.8964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10643  Z= 0.156
  Angle     :  0.775  16.252  14500  Z= 0.382
  Chirality :  0.050   0.458   1573
  Planarity :  0.005   0.058   1856
  Dihedral  :  6.585  58.636   1583
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.38 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 23.02 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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 are not related in a simple way.
  whole: -2.25 (0.22), residues: 1269
  helix: -0.38 (0.25), residues: 417
  sheet: -2.35 (0.59), residues: 70
  loop : -2.14 (0.21), residues: 782

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 563 
 TYR   0.022   0.002   TYR A 199 
 PHE   0.023   0.002   PHE B 338 
 TRP   0.020   0.002   TRP A 461 
 HIS   0.011   0.002   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (10621)
  covalent geometry    : angle       0.74596 (14447)
  SS BOND              : bond        0.00334 (   13)
  SS BOND              : angle       1.08481 (   26)
  hydrogen bonds       : bond        0.04706 (  336)
  hydrogen bonds       : angle       5.59562 (  951)
  link_BETA1-4         : bond        0.02937 (    2)
  link_BETA1-4         : angle       7.19894 (    6)
  link_NAG-ASN         : bond        0.00706 (    7)
  link_NAG-ASN         : angle       3.99940 (   21)

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

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

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8706 (tt)
REVERT: A  176 LEU cc_start: 0.7848 (mt) cc_final: 0.7520 (mt)
REVERT: A  358 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8596 (mm)
REVERT: A  360 MET cc_start: 0.8295 (pmm) cc_final: 0.7946 (pmm)
REVERT: A  434 THR cc_start: 0.8496 (m) cc_final: 0.8221 (p)
REVERT: A  446 ILE cc_start: 0.8864 (tt) cc_final: 0.8350 (pt)
REVERT: A  503 LEU cc_start: 0.8672 (tt) cc_final: 0.7889 (mp)
REVERT: A  583 PRO cc_start: 0.8256 (Cg_exo) cc_final: 0.8049 (Cg_endo)
REVERT: B   60 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6553 (t80)
REVERT: B  132 ASN cc_start: 0.3561 (OUTLIER) cc_final: 0.3173 (m-40)
REVERT: B  325 PHE cc_start: 0.2765 (m-80) cc_final: 0.2077 (m-80)
REVERT: B  656 TYR cc_start: 0.6826 (t80) cc_final: 0.6618 (t80)
  outliers start: 27
  outliers final: 18
  residues processed: 124
  average time/residue: 0.0918
  time to fit residues: 16.6734
Evaluate side-chains
  116 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain B residue   60 TYR
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  476 CYS
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  508 VAL
Chi-restraints excluded: chain B residue  534 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0870
   chunk 57 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   chunk 65 optimal weight:   30.0000
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 121 ASN
B 210 ASN
** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.107257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.085679 restraints weight = 54473.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.088218 restraints weight = 31069.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.089885 restraints weight = 20982.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.090913 restraints weight = 15798.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.091608 restraints weight = 13031.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.9104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10643  Z= 0.143
  Angle     :  0.782  16.732  14500  Z= 0.384
  Chirality :  0.052   0.434   1573
  Planarity :  0.005   0.057   1856
  Dihedral  :  6.320  55.204   1583
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 18.83
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.51 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 23.29 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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 are not related in a simple way.
  whole: -2.08 (0.22), residues: 1269
  helix: -0.22 (0.25), residues: 404
  sheet: -2.33 (0.59), residues: 70
  loop : -2.01 (0.21), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  22 
 TYR   0.048   0.002   TYR A 243 
 PHE   0.034   0.002   PHE B 191 
 TRP   0.017   0.001   TRP A 328 
 HIS   0.042   0.002   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (10621)
  covalent geometry    : angle       0.75333 (14447)
  SS BOND              : bond        0.00292 (   13)
  SS BOND              : angle       1.07610 (   26)
  hydrogen bonds       : bond        0.04696 (  336)
  hydrogen bonds       : angle       5.51245 (  951)
  link_BETA1-4         : bond        0.03161 (    2)
  link_BETA1-4         : angle       7.36075 (    6)
  link_NAG-ASN         : bond        0.01022 (    7)
  link_NAG-ASN         : angle       3.80674 (   21)

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

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

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2538 Ramachandran restraints generated.
    1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8686 (tt)
REVERT: A  176 LEU cc_start: 0.7882 (mt) cc_final: 0.7571 (mt)
REVERT: A  270 MET cc_start: 0.4583 (tpp) cc_final: 0.4288 (tpp)
REVERT: A  328 TRP cc_start: 0.7000 (m100) cc_final: 0.6510 (m100)
REVERT: A  358 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8574 (mm)
REVERT: A  360 MET cc_start: 0.8324 (pmm) cc_final: 0.8041 (pmm)
REVERT: A  401 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.7607 (m-70)
REVERT: A  434 THR cc_start: 0.8598 (m) cc_final: 0.8349 (p)
REVERT: A  446 ILE cc_start: 0.8827 (tt) cc_final: 0.8313 (pt)
REVERT: A  503 LEU cc_start: 0.8719 (tt) cc_final: 0.7932 (mp)
REVERT: B   60 TYR cc_start: 0.6812 (OUTLIER) cc_final: 0.6582 (t80)
REVERT: B  132 ASN cc_start: 0.3452 (OUTLIER) cc_final: 0.3099 (m110)
REVERT: B  325 PHE cc_start: 0.2674 (m-80) cc_final: 0.2092 (m-80)
REVERT: B  656 TYR cc_start: 0.6930 (t80) cc_final: 0.6728 (t80)
  outliers start: 27
  outliers final: 18
  residues processed: 121
  average time/residue: 0.0946
  time to fit residues: 16.5381
Evaluate side-chains
  118 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  432 ASN
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain B residue   60 TYR
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain B residue  132 ASN
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  476 CYS
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  534 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 72 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 80 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0470
   chunk 90 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 124 optimal weight:    0.7980
   overall best weight:    1.2880

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 210 ASN
** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.106234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.084536 restraints weight = 54967.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.087149 restraints weight = 31426.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.088755 restraints weight = 21146.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.089796 restraints weight = 15939.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.090291 restraints weight = 13093.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7100
moved from start:          0.9300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10643  Z= 0.146
  Angle     :  0.775  16.331  14500  Z= 0.383
  Chirality :  0.051   0.439   1573
  Planarity :  0.006   0.062   1856
  Dihedral  :  6.199  54.900   1583
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 18.83
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.67 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 23.38 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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 are not related in a simple way.
  whole: -2.10 (0.22), residues: 1269
  helix: -0.29 (0.25), residues: 406
  sheet: -2.44 (0.65), residues: 51
  loop : -2.02 (0.21), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 563 
 TYR   0.036   0.002   TYR A 243 
 PHE   0.030   0.002   PHE B 191 
 TRP   0.016   0.001   TRP A 461 
 HIS   0.053   0.003   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10621)
  covalent geometry    : angle       0.75018 (14447)
  SS BOND              : bond        0.00282 (   13)
  SS BOND              : angle       1.10845 (   26)
  hydrogen bonds       : bond        0.04675 (  336)
  hydrogen bonds       : angle       5.47727 (  951)
  link_BETA1-4         : bond        0.02977 (    2)
  link_BETA1-4         : angle       7.19424 (    6)
  link_NAG-ASN         : bond        0.00680 (    7)
  link_NAG-ASN         : angle       3.32122 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2370.60 seconds
wall clock time: 41 minutes 28.57 seconds (2488.57 seconds total)