Starting phenix.real_space_refine
on Tue Mar  3 14:59:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xvg_33486/03_2026/7xvg_33486.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xvg_33486/03_2026/7xvg_33486.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xvg_33486/03_2026/7xvg_33486.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xvg_33486/03_2026/7xvg_33486.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xvg_33486/03_2026/7xvg_33486.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xvg_33486/03_2026/7xvg_33486.map"
  }
  resolution = 3.6
  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=   0.001 sd=   0.047
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      26      5.16       5
     C    4160      2.51       5
     N    1066      2.21       5
     O    1186      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  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: 6438
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3327
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 20, 'TRANS': 394}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 379, 3111
          Classifications: {'peptide': 379}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 368}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
  Time building chain proxies: 1.22, per 1000 atoms: 0.19
  Number of scatterers: 6438
  At special positions: 0
  Unit cell: (75.6, 94.08, 110.04, 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      26     16.00
     O    1186      8.00
     N    1066      7.00
     C    4160      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 237.1 milliseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1510

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 5 sheets defined
      50.5% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 434 through 438
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 469 through 482
    Processing helix  chain 'A' and resid 502 through 514
      removed outlier: 3.835A  pdb=" N   ASP A 507 " --> pdb=" O   ASP A 503 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LEU A 508 " --> pdb=" O   MET A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 598
      removed outlier: 3.532A  pdb=" N   LEU A 598 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 621
      removed outlier: 3.701A  pdb=" N   ILE A 618 " --> pdb=" O   PRO A 615 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   GLY A 619 " --> pdb=" O   MET A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 665
    Processing helix  chain 'A' and resid 680 through 687
      removed outlier: 3.672A  pdb=" N   VAL A 684 " --> pdb=" O   ASP A 680 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU A 687 " --> pdb=" O   PHE A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 690
      No H-bonds generated for 'chain 'A' and resid 688 through 690'
    Processing helix  chain 'A' and resid 707 through 718
      removed outlier: 4.170A  pdb=" N   LEU A 711 " --> pdb=" O   MET A 707 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLU A 713 " --> pdb=" O   LYS A 709 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   SER A 716 " --> pdb=" O   GLU A 712 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   MET A 718 " --> pdb=" O   SER A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 786 through 792
    Processing helix  chain 'A' and resid 804 through 810
      removed outlier: 3.833A  pdb=" N   PHE A 808 " --> pdb=" O   ASN A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 844
      removed outlier: 3.719A  pdb=" N   PHE A 844 " --> pdb=" O   PRO A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 864
      removed outlier: 3.795A  pdb=" N   ILE A 864 " --> pdb=" O   ALA A 861 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 150
      removed outlier: 4.252A  pdb=" N   TYR B 148 " --> pdb=" O   ASP B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 193
      removed outlier: 3.560A  pdb=" N   ASN B 189 " --> pdb=" O   PHE B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 199
      removed outlier: 4.365A  pdb=" N   ILE B 198 " --> pdb=" O   LYS B 194 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   LEU B 199 " --> pdb=" O   ASP B 195 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 194 through 199'
    Processing helix  chain 'B' and resid 211 through 226
    Processing helix  chain 'B' and resid 229 through 244
      removed outlier: 3.984A  pdb=" N   ILE B 234 " --> pdb=" O   PRO B 230 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   GLU B 235 " --> pdb=" O   GLU B 231 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL B 240 " --> pdb=" O   GLU B 236 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LYS B 243 " --> pdb=" O   LYS B 239 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL B 244 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 275
      removed outlier: 3.552A  pdb=" N   ILE B 262 " --> pdb=" O   PHE B 258 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLN B 263 " --> pdb=" O   ASN B 259 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ILE B 270 " --> pdb=" O   ALA B 266 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   HIS B 271 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS B 275 " --> pdb=" O   HIS B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 289
    Processing helix  chain 'B' and resid 290 through 317
      removed outlier: 3.530A  pdb=" N   LYS B 295 " --> pdb=" O   ASP B 291 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   VAL B 302 " --> pdb=" O   ALA B 298 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LYS B 308 " --> pdb=" O   THR B 304 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   PHE B 310 " --> pdb=" O   LYS B 306 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   ASP B 311 " --> pdb=" O   MET B 307 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   SER B 312 " --> pdb=" O   LYS B 308 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LYS B 315 " --> pdb=" O   ASP B 311 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   MET B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 322
      removed outlier: 3.680A  pdb=" N   ILE B 322 " --> pdb=" O   ASN B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 330
      removed outlier: 4.281A  pdb=" N   ASP B 328 " --> pdb=" O   GLU B 325 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B 329 " --> pdb=" O   MET B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 335
      removed outlier: 3.565A  pdb=" N   SER B 334 " --> pdb=" O   TRP B 331 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   HIS B 335 " --> pdb=" O   GLN B 332 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 331 through 335'
    Processing helix  chain 'B' and resid 336 through 347
      removed outlier: 4.094A  pdb=" N   LEU B 343 " --> pdb=" O   PHE B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 365
      removed outlier: 3.835A  pdb=" N   SER B 351 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER B 352 " --> pdb=" O   ALA B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 392
    Processing helix  chain 'B' and resid 393 through 396
    Processing helix  chain 'B' and resid 403 through 419
    Processing helix  chain 'B' and resid 423 through 441
      removed outlier: 3.597A  pdb=" N   PHE B 441 " --> pdb=" O   LEU B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 455
      removed outlier: 3.757A  pdb=" N   LEU B 452 " --> pdb=" O   PHE B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 483
    Processing helix  chain 'B' and resid 508 through 529
      removed outlier: 4.253A  pdb=" N   LYS B 512 " --> pdb=" O   LYS B 508 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   GLU B 513 " --> pdb=" O   HIS B 509 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   VAL B 516 " --> pdb=" O   LYS B 512 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   SER B 517 " --> pdb=" O   GLU B 513 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   TYR B 518 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ARG B 529 " --> pdb=" O   THR B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 553
      removed outlier: 3.556A  pdb=" N   LEU B 544 " --> pdb=" O   CYS B 540 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   SER B 553 " --> pdb=" O   ASN B 549 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 445
      removed outlier: 6.538A  pdb=" N   VAL A 496 " --> pdb=" O   ILE A 490 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   ILE A 490 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG A 500 " --> pdb=" O   GLN A 486 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLN A 486 " --> pdb=" O   ARG A 500 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 583
    Processing sheet with id=AA3, first strand: chain 'A' and resid 626 through 628
      removed outlier: 6.848A  pdb=" N   LEU A 627 " --> pdb=" O   TYR A 651 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ASP A 672 " --> pdb=" O   LEU A 650 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   ARG A 697 " --> pdb=" O   ASP A 672 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP A 699 " --> pdb=" O   LEU A 674 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ASP A 725 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 799 through 802
      removed outlier: 7.512A  pdb=" N   LEU A 800 " --> pdb=" O   ARG A 833 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 856 through 859
      removed outlier: 3.857A  pdb=" N   PHE A 857 " --> pdb=" O   ARG A 881 " (cutoff:3.500A)

    230 hydrogen bonds defined for protein.
    645 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.88

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1132
        1.32 -     1.44: 1657
        1.44 -     1.57: 3744
        1.57 -     1.69: 1
        1.69 -     1.81: 42
  Bond restraints: 6576
  Sorted by residual:
  bond pdb=" N   LEU A 879 "
       pdb=" CA  LEU A 879 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.036 1.36e-02 5.41e+03 6.95e+00
  bond pdb=" C   PRO A 877 "
       pdb=" O   PRO A 877 "
    ideal  model  delta    sigma   weight residual
    1.235  1.203  0.032 1.30e-02 5.92e+03 6.21e+00
  bond pdb=" N   SER A 878 "
       pdb=" CA  SER A 878 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 6.11e+00
  bond pdb=" CA  SER A 878 "
       pdb=" CB  SER A 878 "
    ideal  model  delta    sigma   weight residual
    1.530  1.488  0.042 1.69e-02 3.50e+03 6.11e+00
  bond pdb=" N   LEU A 690 "
       pdb=" CA  LEU A 690 "
    ideal  model  delta    sigma   weight residual
    1.462  1.490 -0.028 1.23e-02 6.61e+03 5.05e+00
  ... (remaining 6571 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 8666
        2.05 -     4.10: 179
        4.10 -     6.15: 28
        6.15 -     8.19: 6
        8.19 -    10.24: 3
  Bond angle restraints: 8882
  Sorted by residual:
  angle pdb=" N   ILE B 318 "
        pdb=" CA  ILE B 318 "
        pdb=" C   ILE B 318 "
      ideal   model   delta    sigma   weight residual
     111.91  108.20    3.71 8.90e-01 1.26e+00 1.73e+01
  angle pdb=" N   GLU A 478 "
        pdb=" CA  GLU A 478 "
        pdb=" CB  GLU A 478 "
      ideal   model   delta    sigma   weight residual
     110.28  116.49   -6.21 1.55e+00 4.16e-01 1.61e+01
  angle pdb=" N   ARG A 689 "
        pdb=" CA  ARG A 689 "
        pdb=" C   ARG A 689 "
      ideal   model   delta    sigma   weight residual
     112.89  108.19    4.70 1.24e+00 6.50e-01 1.43e+01
  angle pdb=" C   ASN A 477 "
        pdb=" N   GLU A 478 "
        pdb=" CA  GLU A 478 "
      ideal   model   delta    sigma   weight residual
     120.31  115.12    5.19 1.52e+00 4.33e-01 1.17e+01
  angle pdb=" C   PRO A 850 "
        pdb=" N   ARG A 851 "
        pdb=" CA  ARG A 851 "
      ideal   model   delta    sigma   weight residual
     122.56  117.89    4.67 1.50e+00 4.44e-01 9.71e+00
  ... (remaining 8877 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3547
       17.95 -    35.90: 360
       35.90 -    53.86: 45
       53.86 -    71.81: 10
       71.81 -    89.76: 5
  Dihedral angle restraints: 3967
    sinusoidal: 1638
      harmonic: 2329
  Sorted by residual:
  dihedral pdb=" CA  LEU A 693 "
           pdb=" C   LEU A 693 "
           pdb=" N   ARG A 694 "
           pdb=" CA  ARG A 694 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.18   20.82     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CG  ARG A 689 "
           pdb=" CD  ARG A 689 "
           pdb=" NE  ARG A 689 "
           pdb=" CZ  ARG A 689 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -32.90  -57.10     2      1.50e+01 4.44e-03 1.50e+01
  dihedral pdb=" CA  LEU B 267 "
           pdb=" C   LEU B 267 "
           pdb=" N   GLN B 268 "
           pdb=" CA  GLN B 268 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.84   17.16     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 3964 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 761
       0.052 -    0.103: 195
       0.103 -    0.155: 37
       0.155 -    0.207: 0
       0.207 -    0.259: 3
  Chirality restraints: 996
  Sorted by residual:
  chirality pdb=" CA  ARG A 689 "
            pdb=" N   ARG A 689 "
            pdb=" C   ARG A 689 "
            pdb=" CB  ARG A 689 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CB  ILE A 869 "
            pdb=" CA  ILE A 869 "
            pdb=" CG1 ILE A 869 "
            pdb=" CG2 ILE A 869 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  LEU A 879 "
            pdb=" N   LEU A 879 "
            pdb=" C   LEU A 879 "
            pdb=" CB  LEU A 879 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 993 not shown)

  Planarity restraints: 1116
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 688 "   -0.020 2.00e-02 2.50e+03   4.00e-02 1.60e+01
        pdb=" C   GLY A 688 "    0.069 2.00e-02 2.50e+03
        pdb=" O   GLY A 688 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ARG A 689 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 876 "    0.018 2.00e-02 2.50e+03   3.51e-02 1.24e+01
        pdb=" C   LEU A 876 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   LEU A 876 "    0.022 2.00e-02 2.50e+03
        pdb=" N   PRO A 877 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 689 "   -0.161 9.50e-02 1.11e+02   7.23e-02 3.21e+00
        pdb=" NE  ARG A 689 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 689 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 689 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 689 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1113 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 84
        2.64 -     3.20: 6170
        3.20 -     3.77: 9567
        3.77 -     4.33: 12956
        4.33 -     4.90: 20683
  Nonbonded interactions: 49460
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU A 879 "
            pdb=" N   GLN A 880 "
     model   vdw
     2.074 3.540
  nonbonded pdb=" O   THR A 691 "
            pdb=" OG1 THR A 691 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" O   GLU B 222 "
            pdb=" OG1 THR B 226 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OG  SER A 842 "
            pdb=" O   ASN A 868 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   GLU A 713 "
            pdb=" OG  SER A 716 "
     model   vdw
     2.265 3.040
  ... (remaining 49455 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.930
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6576  Z= 0.178
  Angle     :  0.728  10.242   8882  Z= 0.381
  Chirality :  0.048   0.259    996
  Planarity :  0.005   0.072   1116
  Dihedral  : 14.260  89.760   2457
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.90 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.83 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.31), residues: 780
  helix:  0.51 (0.30), residues: 325
  sheet: -2.62 (0.73), residues: 59
  loop : -1.30 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 500 
 TYR   0.015   0.001   TYR A 460 
 PHE   0.028   0.002   PHE B 233 
 TRP   0.013   0.002   TRP A 856 
 HIS   0.005   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6576)
  covalent geometry    : angle       0.72776 ( 8882)
  hydrogen bonds       : bond        0.19403 (  230)
  hydrogen bonds       : angle       6.18500 (  645)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  486 GLN cc_start: 0.8144 (pm20) cc_final: 0.7928 (pm20)
REVERT: B  195 ASP cc_start: 0.8268 (m-30) cc_final: 0.7995 (t0)
REVERT: B  501 PHE cc_start: 0.7888 (m-80) cc_final: 0.7556 (m-80)
REVERT: B  516 VAL cc_start: 0.8205 (t) cc_final: 0.7781 (t)
  outliers start: 2
  outliers final: 2
  residues processed: 107
  average time/residue: 0.0690
  time to fit residues: 10.2695
Evaluate side-chains
  87 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  689 ARG
Chi-restraints excluded: chain A residue  691 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 729 ASN
A 875 HIS
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.154936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.120836 restraints weight = 11345.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.123498 restraints weight = 6274.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.124205 restraints weight = 5516.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.124864 restraints weight = 4101.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.125214 restraints weight = 3829.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6576  Z= 0.128
  Angle     :  0.660  10.131   8882  Z= 0.322
  Chirality :  0.045   0.137    996
  Planarity :  0.004   0.040   1116
  Dihedral  :  4.945  59.491    859
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.34 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.30), residues: 780
  helix:  0.51 (0.29), residues: 333
  sheet: -2.77 (0.69), residues: 61
  loop : -1.37 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 448 
 TYR   0.015   0.001   TYR B 383 
 PHE   0.021   0.001   PHE A 703 
 TRP   0.016   0.001   TRP A 453 
 HIS   0.007   0.001   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6576)
  covalent geometry    : angle       0.66041 ( 8882)
  hydrogen bonds       : bond        0.04569 (  230)
  hydrogen bonds       : angle       4.60492 (  645)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  486 GLN cc_start: 0.8357 (pm20) cc_final: 0.8135 (pm20)
REVERT: A  634 ILE cc_start: 0.6932 (tp) cc_final: 0.6688 (tp)
REVERT: A  682 ASP cc_start: 0.8310 (p0) cc_final: 0.7772 (p0)
REVERT: A  809 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8014 (mm-30)
REVERT: B  195 ASP cc_start: 0.8473 (m-30) cc_final: 0.8187 (t0)
REVERT: B  233 PHE cc_start: 0.7393 (t80) cc_final: 0.7159 (t80)
REVERT: B  501 PHE cc_start: 0.8031 (m-80) cc_final: 0.7585 (m-10)
  outliers start: 8
  outliers final: 4
  residues processed: 99
  average time/residue: 0.0675
  time to fit residues: 9.3797
Evaluate side-chains
  90 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  729 ASN
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain B residue  465 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   chunk 75 optimal weight:    8.9990
   chunk 1 optimal weight:    0.0870
   chunk 11 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0670
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 729 ASN
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.155667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.118096 restraints weight = 10939.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.122098 restraints weight = 5914.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.124610 restraints weight = 4141.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.126063 restraints weight = 3374.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.126766 restraints weight = 3007.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6576  Z= 0.112
  Angle     :  0.603   9.710   8882  Z= 0.293
  Chirality :  0.043   0.139    996
  Planarity :  0.004   0.038   1116
  Dihedral  :  4.291  18.065    854
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.83 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.31), residues: 780
  helix:  0.53 (0.29), residues: 333
  sheet: -2.42 (0.70), residues: 59
  loop : -1.31 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 689 
 TYR   0.012   0.001   TYR B 383 
 PHE   0.022   0.001   PHE A 703 
 TRP   0.012   0.001   TRP A 453 
 HIS   0.004   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6576)
  covalent geometry    : angle       0.60253 ( 8882)
  hydrogen bonds       : bond        0.04134 (  230)
  hydrogen bonds       : angle       4.44926 (  645)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: A  482 ARG cc_start: 0.8790 (mmp80) cc_final: 0.8366 (mmp80)
REVERT: A  486 GLN cc_start: 0.8377 (pm20) cc_final: 0.8124 (pm20)
REVERT: A  585 GLU cc_start: 0.7800 (pp20) cc_final: 0.7430 (pm20)
REVERT: A  634 ILE cc_start: 0.6843 (tp) cc_final: 0.6560 (tp)
REVERT: A  682 ASP cc_start: 0.8185 (p0) cc_final: 0.7824 (p0)
REVERT: B  501 PHE cc_start: 0.7830 (m-80) cc_final: 0.7512 (m-10)
  outliers start: 16
  outliers final: 8
  residues processed: 101
  average time/residue: 0.0634
  time to fit residues: 9.1130
Evaluate side-chains
  90 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  509 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 76 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    1.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.151332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.117565 restraints weight = 11296.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.119726 restraints weight = 6420.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.120439 restraints weight = 5115.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.120835 restraints weight = 4537.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.121368 restraints weight = 4121.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6576  Z= 0.169
  Angle     :  0.644   8.775   8882  Z= 0.323
  Chirality :  0.045   0.141    996
  Planarity :  0.004   0.040   1116
  Dihedral  :  4.425  18.992    854
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.14 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.31), residues: 780
  helix:  0.44 (0.29), residues: 334
  sheet: -2.84 (0.65), residues: 65
  loop : -1.27 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 689 
 TYR   0.017   0.001   TYR A 799 
 PHE   0.020   0.002   PHE A 703 
 TRP   0.012   0.001   TRP A 856 
 HIS   0.007   0.001   HIS B 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 6576)
  covalent geometry    : angle       0.64427 ( 8882)
  hydrogen bonds       : bond        0.04670 (  230)
  hydrogen bonds       : angle       4.56991 (  645)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  486 GLN cc_start: 0.8357 (pm20) cc_final: 0.7954 (pm20)
REVERT: A  585 GLU cc_start: 0.7852 (pp20) cc_final: 0.7192 (pm20)
REVERT: A  634 ILE cc_start: 0.7152 (tp) cc_final: 0.6914 (tp)
REVERT: B  437 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8340 (tt)
REVERT: B  501 PHE cc_start: 0.7887 (m-80) cc_final: 0.7499 (m-10)
  outliers start: 22
  outliers final: 13
  residues processed: 109
  average time/residue: 0.0633
  time to fit residues: 9.8080
Evaluate side-chains
  99 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  509 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 28 optimal weight:    0.3980
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0040
   chunk 17 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    1.2396

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

Flipped N/Q/H residues before XYZ refinement:
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.152236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.118130 restraints weight = 11257.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.120762 restraints weight = 6463.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.121353 restraints weight = 5702.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.122011 restraints weight = 4293.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.122284 restraints weight = 4040.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6576  Z= 0.139
  Angle     :  0.645   8.378   8882  Z= 0.317
  Chirality :  0.044   0.158    996
  Planarity :  0.004   0.039   1116
  Dihedral  :  4.394  21.293    854
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.79 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.31), residues: 780
  helix:  0.49 (0.29), residues: 334
  sheet: -2.85 (0.62), residues: 69
  loop : -1.22 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 446 
 TYR   0.014   0.001   TYR B 383 
 PHE   0.019   0.002   PHE A 703 
 TRP   0.011   0.001   TRP B 356 
 HIS   0.006   0.001   HIS B 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6576)
  covalent geometry    : angle       0.64511 ( 8882)
  hydrogen bonds       : bond        0.04381 (  230)
  hydrogen bonds       : angle       4.47610 (  645)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  585 GLU cc_start: 0.7903 (pp20) cc_final: 0.7314 (pm20)
REVERT: A  721 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6979 (mt)
REVERT: B  437 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8327 (tt)
REVERT: B  501 PHE cc_start: 0.7911 (m-80) cc_final: 0.7509 (m-10)
  outliers start: 20
  outliers final: 14
  residues processed: 104
  average time/residue: 0.0597
  time to fit residues: 8.8919
Evaluate side-chains
  98 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  484 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 53 optimal weight:    0.7980
   chunk 45 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 72 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.152013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.117627 restraints weight = 11268.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.120010 restraints weight = 6649.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.120596 restraints weight = 5629.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.121312 restraints weight = 4514.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.121563 restraints weight = 4269.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6576  Z= 0.140
  Angle     :  0.649  11.567   8882  Z= 0.316
  Chirality :  0.044   0.133    996
  Planarity :  0.004   0.042   1116
  Dihedral  :  4.342  19.509    854
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.03 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.31), residues: 780
  helix:  0.56 (0.29), residues: 334
  sheet: -2.78 (0.62), residues: 67
  loop : -1.19 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 186 
 TYR   0.013   0.001   TYR B 383 
 PHE   0.018   0.001   PHE B 233 
 TRP   0.011   0.001   TRP B 356 
 HIS   0.009   0.001   HIS B 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6576)
  covalent geometry    : angle       0.64932 ( 8882)
  hydrogen bonds       : bond        0.04294 (  230)
  hydrogen bonds       : angle       4.39027 (  645)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 GLU cc_start: 0.7840 (pp20) cc_final: 0.7633 (pp20)
REVERT: A  585 GLU cc_start: 0.7938 (pp20) cc_final: 0.7367 (pm20)
REVERT: A  718 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.7111 (pmm)
REVERT: A  721 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7053 (mt)
REVERT: B  437 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8351 (tt)
REVERT: B  501 PHE cc_start: 0.7919 (m-80) cc_final: 0.7506 (m-10)
  outliers start: 23
  outliers final: 15
  residues processed: 103
  average time/residue: 0.0617
  time to fit residues: 8.9777
Evaluate side-chains
  103 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  718 MET
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  721 LEU
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 71 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.152543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.118728 restraints weight = 10948.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.119555 restraints weight = 6433.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.120410 restraints weight = 5498.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.121079 restraints weight = 4780.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.121442 restraints weight = 4475.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6576  Z= 0.147
  Angle     :  0.661  11.336   8882  Z= 0.325
  Chirality :  0.044   0.136    996
  Planarity :  0.004   0.038   1116
  Dihedral  :  4.345  20.737    854
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 18.34 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.31), residues: 780
  helix:  0.58 (0.29), residues: 334
  sheet: -2.74 (0.63), residues: 67
  loop : -1.18 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 186 
 TYR   0.014   0.001   TYR B 383 
 PHE   0.018   0.002   PHE B 233 
 TRP   0.012   0.001   TRP B 356 
 HIS   0.008   0.001   HIS B 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6576)
  covalent geometry    : angle       0.66135 ( 8882)
  hydrogen bonds       : bond        0.04345 (  230)
  hydrogen bonds       : angle       4.45168 (  645)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  585 GLU cc_start: 0.7921 (pp20) cc_final: 0.7158 (pm20)
REVERT: A  713 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7779 (pm20)
REVERT: B  232 GLU cc_start: 0.8210 (tp30) cc_final: 0.7891 (tp30)
REVERT: B  318 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8340 (pt)
REVERT: B  437 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8378 (tt)
REVERT: B  501 PHE cc_start: 0.7945 (m-80) cc_final: 0.7521 (m-10)
  outliers start: 27
  outliers final: 16
  residues processed: 107
  average time/residue: 0.0612
  time to fit residues: 9.3193
Evaluate side-chains
  107 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  453 TRP
Chi-restraints excluded: chain A residue  713 GLU
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.153668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.121452 restraints weight = 10885.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.119733 restraints weight = 6901.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.121004 restraints weight = 6776.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.122244 restraints weight = 5007.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.122719 restraints weight = 4402.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6576  Z= 0.122
  Angle     :  0.667  11.315   8882  Z= 0.321
  Chirality :  0.043   0.135    996
  Planarity :  0.004   0.041   1116
  Dihedral  :  4.247  19.130    854
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 19.72 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.31), residues: 780
  helix:  0.65 (0.29), residues: 333
  sheet: -2.78 (0.62), residues: 69
  loop : -1.10 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 186 
 TYR   0.014   0.001   TYR B 383 
 PHE   0.018   0.001   PHE B 233 
 TRP   0.011   0.001   TRP B 356 
 HIS   0.005   0.001   HIS B 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6576)
  covalent geometry    : angle       0.66667 ( 8882)
  hydrogen bonds       : bond        0.04067 (  230)
  hydrogen bonds       : angle       4.35512 (  645)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  585 GLU cc_start: 0.7848 (pp20) cc_final: 0.7128 (pm20)
REVERT: A  713 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7749 (pm20)
REVERT: B  232 GLU cc_start: 0.8105 (tp30) cc_final: 0.7833 (tp30)
REVERT: B  318 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8363 (pt)
REVERT: B  437 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8739 (tt)
REVERT: B  501 PHE cc_start: 0.7877 (m-80) cc_final: 0.7506 (m-10)
  outliers start: 22
  outliers final: 15
  residues processed: 107
  average time/residue: 0.0604
  time to fit residues: 9.1974
Evaluate side-chains
  105 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  656 MET
Chi-restraints excluded: chain A residue  713 GLU
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 74 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 71 optimal weight:    5.9990
   chunk 51 optimal weight:    0.4980
   chunk 62 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.153575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.120170 restraints weight = 11042.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.121119 restraints weight = 6387.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.122110 restraints weight = 5387.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.122759 restraints weight = 4536.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.123212 restraints weight = 4254.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6576  Z= 0.131
  Angle     :  0.686  11.502   8882  Z= 0.332
  Chirality :  0.044   0.148    996
  Planarity :  0.004   0.043   1116
  Dihedral  :  4.287  21.940    854
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.14 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.31), residues: 780
  helix:  0.63 (0.29), residues: 333
  sheet: -2.70 (0.63), residues: 67
  loop : -1.11 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 186 
 TYR   0.015   0.001   TYR A 460 
 PHE   0.017   0.001   PHE B 448 
 TRP   0.011   0.001   TRP B 356 
 HIS   0.006   0.001   HIS B 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6576)
  covalent geometry    : angle       0.68560 ( 8882)
  hydrogen bonds       : bond        0.04036 (  230)
  hydrogen bonds       : angle       4.34563 (  645)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  440 GLU cc_start: 0.7914 (tt0) cc_final: 0.7217 (pm20)
REVERT: A  441 ASP cc_start: 0.7963 (p0) cc_final: 0.7751 (p0)
REVERT: A  585 GLU cc_start: 0.7848 (pp20) cc_final: 0.7142 (pm20)
REVERT: A  713 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7791 (pm20)
REVERT: B  318 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8354 (pt)
REVERT: B  472 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7741 (mm-30)
REVERT: B  501 PHE cc_start: 0.7830 (m-80) cc_final: 0.7481 (m-10)
  outliers start: 21
  outliers final: 17
  residues processed: 105
  average time/residue: 0.0676
  time to fit residues: 9.9733
Evaluate side-chains
  106 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  656 MET
Chi-restraints excluded: chain A residue  713 GLU
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 49 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 76 optimal weight:    0.0470
   chunk 19 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0870
   chunk 69 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.154529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.120292 restraints weight = 11044.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.120925 restraints weight = 6582.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.121534 restraints weight = 5321.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.122076 restraints weight = 4823.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.122753 restraints weight = 4291.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6576  Z= 0.116
  Angle     :  0.684  11.670   8882  Z= 0.329
  Chirality :  0.042   0.137    996
  Planarity :  0.004   0.039   1116
  Dihedral  :  4.171  17.585    854
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 20.55 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.31), residues: 780
  helix:  0.70 (0.29), residues: 333
  sheet: -2.70 (0.61), residues: 68
  loop : -1.12 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 186 
 TYR   0.013   0.001   TYR B 383 
 PHE   0.015   0.001   PHE A 703 
 TRP   0.011   0.001   TRP B 356 
 HIS   0.011   0.001   HIS B 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6576)
  covalent geometry    : angle       0.68398 ( 8882)
  hydrogen bonds       : bond        0.03718 (  230)
  hydrogen bonds       : angle       4.28418 (  645)

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  440 GLU cc_start: 0.7835 (tt0) cc_final: 0.7033 (pm20)
REVERT: A  585 GLU cc_start: 0.7872 (pp20) cc_final: 0.7080 (pm20)
REVERT: A  628 ASP cc_start: 0.8310 (t0) cc_final: 0.8037 (t0)
REVERT: A  713 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7912 (pm20)
REVERT: B  318 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8353 (pt)
REVERT: B  437 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8627 (tt)
REVERT: B  501 PHE cc_start: 0.7964 (m-80) cc_final: 0.7538 (m-10)
  outliers start: 19
  outliers final: 15
  residues processed: 101
  average time/residue: 0.0619
  time to fit residues: 8.9810
Evaluate side-chains
  107 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  656 MET
Chi-restraints excluded: chain A residue  713 GLU
Chi-restraints excluded: chain A residue  719 TYR
Chi-restraints excluded: chain A residue  725 ASP
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  779 THR
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  869 ILE
Chi-restraints excluded: chain A residue  876 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  465 LEU
Chi-restraints excluded: chain B residue  509 HIS
Chi-restraints excluded: chain B residue  521 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.0570
   chunk 29 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0670
   chunk 5 optimal weight:   20.0000
   chunk 42 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 73 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   chunk 68 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.5836

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

Flipped N/Q/H residues before XYZ refinement:
** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.154563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.120752 restraints weight = 11125.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.120941 restraints weight = 6573.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.122153 restraints weight = 5544.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.123186 restraints weight = 4451.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.123563 restraints weight = 4102.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6576  Z= 0.117
  Angle     :  0.690  11.606   8882  Z= 0.329
  Chirality :  0.042   0.136    996
  Planarity :  0.004   0.045   1116
  Dihedral  :  4.121  15.986    854
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.69 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.31), residues: 780
  helix:  0.73 (0.29), residues: 333
  sheet: -2.40 (0.65), residues: 63
  loop : -1.18 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 186 
 TYR   0.015   0.001   TYR A 460 
 PHE   0.018   0.001   PHE B 448 
 TRP   0.010   0.001   TRP B 356 
 HIS   0.007   0.001   HIS B 509 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6576)
  covalent geometry    : angle       0.69002 ( 8882)
  hydrogen bonds       : bond        0.03678 (  230)
  hydrogen bonds       : angle       4.26136 (  645)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1063.78 seconds
wall clock time: 19 minutes 7.71 seconds (1147.71 seconds total)