Starting phenix.real_space_refine
on Wed Mar  4 03:15:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dd4_27334/03_2026/8dd4_27334.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dd4_27334/03_2026/8dd4_27334.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dd4_27334/03_2026/8dd4_27334.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dd4_27334/03_2026/8dd4_27334.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dd4_27334/03_2026/8dd4_27334.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dd4_27334/03_2026/8dd4_27334.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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      73      5.16       5
     C    6624      2.51       5
     N    1807      2.21       5
     O    1922      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10426
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8076
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 981, 8043
          Classifications: {'peptide': 981}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 935}
          Chain breaks: 4
      Conformer: "B"
        Number of residues, atoms: 981, 8043
          Classifications: {'peptide': 981}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 935}
          Chain breaks: 4
          bond proxies already assigned to first conformer: 8187
    Chain: "B"
      Number of atoms: 2329
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2329
          Classifications: {'peptide': 274}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 269}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 18
          Classifications: {'water': 18}
          Link IDs: {None: 17}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  AARG A 617 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 617 " occ=0.50
    residue:
      pdb=" N  AARG A 651 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 651 " occ=0.50
    residue:
      pdb=" N  AARG A 704 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 704 " occ=0.50
  Time building chain proxies: 3.97, per 1000 atoms: 0.38
  Number of scatterers: 10426
  At special positions: 0
  Unit cell: (106.029, 132.804, 112.455, 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      73     16.00
     O    1922      8.00
     N    1807      7.00
     C    6624      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: 0.79
  Conformation dependent library (CDL) restraints added in 756.1 milliseconds
  

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2410

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 10 sheets defined
      51.7% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 54
      removed outlier: 3.509A  pdb=" N   GLU A  52 " --> pdb=" O   GLU A  48 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ARG A  54 " --> pdb=" O   PHE A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 62
    Processing helix  chain 'A' and resid 64 through 68
    Processing helix  chain 'A' and resid 108 through 122
    Processing helix  chain 'A' and resid 124 through 130
      removed outlier: 4.024A  pdb=" N   PHE A 128 " --> pdb=" O   PRO A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 155
      removed outlier: 3.515A  pdb=" N   GLN A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU A 144 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   ASN A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   VAL A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP A 155 " --> pdb=" O   VAL A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 167
      removed outlier: 3.571A  pdb=" N   ALA A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 183
      removed outlier: 3.540A  pdb=" N   TYR A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ASN A 183 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 178 through 183'
    Processing helix  chain 'A' and resid 216 through 229
      removed outlier: 3.589A  pdb=" N   THR A 229 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 290 through 297
    Processing helix  chain 'A' and resid 305 through 309
      removed outlier: 3.733A  pdb=" N   ARG A 309 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 330
      removed outlier: 3.739A  pdb=" N   VAL A 329 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A 330 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 326 through 330'
    Processing helix  chain 'A' and resid 488 through 496
      removed outlier: 3.569A  pdb=" N   ILE A 492 " --> pdb=" O   ASP A 488 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA A 496 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 537
      removed outlier: 3.569A  pdb=" N   ARG A 537 " --> pdb=" O   ALA A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 554
    Processing helix  chain 'A' and resid 557 through 563
      removed outlier: 3.886A  pdb=" N   THR A 560 " --> pdb=" O   TYR A 557 " (cutoff:3.500A)
      Proline residue:  A 562  - end of helix
    Processing helix  chain 'A' and resid 564 through 572
      removed outlier: 3.521A  pdb=" N   VAL A 572 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 589
      removed outlier: 3.632A  pdb=" N   ASP A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 600
      removed outlier: 3.918A  pdb=" N   GLU A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 603
      No H-bonds generated for 'chain 'A' and resid 601 through 603'
    Processing helix  chain 'A' and resid 608 through 623
    Processing helix  chain 'A' and resid 624 through 631
    Processing helix  chain 'A' and resid 631 through 638
    Processing helix  chain 'A' and resid 647 through 658
    Processing helix  chain 'A' and resid 660 through 674
      removed outlier: 3.523A  pdb=" N   PHE A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 696
      removed outlier: 3.782A  pdb=" N   LEU A 687 " --> pdb=" O   ARG A 683 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   GLY A 696 " --> pdb=" O   CYS A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 721
      removed outlier: 4.072A  pdb=" N   LEU A 719 " --> pdb=" O   LEU A 715 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLN A 721 " --> pdb=" O   ASP A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 739
      removed outlier: 3.521A  pdb=" N   GLN A 731 " --> pdb=" O   THR A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 748
      removed outlier: 3.992A  pdb=" N   MET A 745 " --> pdb=" O   ARG A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 828
    Processing helix  chain 'A' and resid 857 through 865
    Processing helix  chain 'A' and resid 875 through 885
      removed outlier: 3.859A  pdb=" N   ASN A 885 " --> pdb=" O   LEU A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 912
    Processing helix  chain 'A' and resid 940 through 944
      removed outlier: 4.237A  pdb=" N   LYS A 944 " --> pdb=" O   LYS A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 957 through 965
      removed outlier: 3.674A  pdb=" N   VAL A 963 " --> pdb=" O   ASP A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 994
      removed outlier: 4.529A  pdb=" N   GLU A 978 " --> pdb=" O   THR A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1005
      removed outlier: 4.143A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1006 through 1009
      removed outlier: 4.165A  pdb=" N   GLY A1009 " --> pdb=" O   LEU A1006 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1006 through 1009'
    Processing helix  chain 'A' and resid 1015 through 1026
      removed outlier: 4.047A  pdb=" N   ILE A1019 " --> pdb=" O   SER A1015 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TYR A1021 " --> pdb=" O   ASP A1017 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ILE A1022 " --> pdb=" O   ASP A1018 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A1026 " --> pdb=" O   ILE A1022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1046
      removed outlier: 3.989A  pdb=" N   LEU A1036 " --> pdb=" O   GLU A1032 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLU A1037 " --> pdb=" O   GLN A1033 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 347
    Processing helix  chain 'B' and resid 385 through 389
      removed outlier: 3.884A  pdb=" N   GLY B 388 " --> pdb=" O   HIS B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 410
      removed outlier: 3.837A  pdb=" N   LEU B 404 " --> pdb=" O   SER B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 437
      removed outlier: 3.545A  pdb=" N   VAL B 437 " --> pdb=" O   GLN B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 504
    Processing helix  chain 'B' and resid 508 through 516
      removed outlier: 3.615A  pdb=" N   PHE B 512 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 588
      removed outlier: 3.525A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 517 " (cutoff:3.500A)
      Proline residue:  B 568  - end of helix
    Processing helix  chain 'B' and resid 591 through 596
      removed outlier: 4.011A  pdb=" N   GLU B 596 " --> pdb=" O   LYS B 592 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 36
      removed outlier: 3.719A  pdb=" N   VAL A  32 " --> pdb=" O   CYS A  24 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU A  34 " --> pdb=" O   VAL A  22 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE A  20 " --> pdb=" O   CYS A  36 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LEU A  99 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   VAL A 101 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A 102 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 212
      removed outlier: 3.584A  pdb=" N   TYR A 207 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 340
      removed outlier: 4.647A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU A 385 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   CYS A 340 " --> pdb=" O   TRP A 383 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   TRP A 383 " --> pdb=" O   CYS A 340 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.523A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.523A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LYS A 353 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU A 402 " --> pdb=" O   ASN A 426 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   ASN A 426 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   LEU A 404 " --> pdb=" O   TRP A 424 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   TRP A 424 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   ILE A 406 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU A 418 " --> pdb=" O   LYS A 410 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 439 through 444
      removed outlier: 3.767A  pdb=" N   GLY A 439 " --> pdb=" O   PHE A 477 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   MET A 441 " --> pdb=" O   LEU A 475 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752
      removed outlier: 3.733A  pdb=" N   PHE A 751 " --> pdb=" O   LEU A 761 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 779 through 784
    Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856
    Processing sheet with id=AB1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 4.106A  pdb=" N   THR B 354 " --> pdb=" O   ARG B 373 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ASN B 377 " --> pdb=" O   LYS B 374 " (cutoff:3.500A)

    486 hydrogen bonds defined for protein.
    1416 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.52

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3414
        1.34 -     1.46: 2343
        1.46 -     1.58: 4756
        1.58 -     1.70: 0
        1.70 -     1.82: 114
  Bond restraints: 10627
  Sorted by residual:
  bond pdb=" CG1 ILE A 819 "
       pdb=" CD1 ILE A 819 "
    ideal  model  delta    sigma   weight residual
    1.513  1.463  0.050 3.90e-02 6.57e+02 1.66e+00
  bond pdb=" C   SER A 199 "
       pdb=" N   PRO A 200 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.029 2.34e-02 1.83e+03 1.57e+00
  bond pdb=" CA  ASP B 337 "
       pdb=" CB  ASP B 337 "
    ideal  model  delta    sigma   weight residual
    1.524  1.541 -0.016 1.53e-02 4.27e+03 1.14e+00
  bond pdb=" CG  LEU A 688 "
       pdb=" CD1 LEU A 688 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.05e+00
  bond pdb=" CB  LYS A 179 "
       pdb=" CG  LYS A 179 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.29e-01
  ... (remaining 10622 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 14047
        1.99 -     3.98: 235
        3.98 -     5.97: 31
        5.97 -     7.96: 10
        7.96 -     9.95: 5
  Bond angle restraints: 14328
  Sorted by residual:
  angle pdb=" C   THR A1052 "
        pdb=" N   THR A1053 "
        pdb=" CA  THR A1053 "
      ideal   model   delta    sigma   weight residual
     121.54  128.42   -6.88 1.91e+00 2.74e-01 1.30e+01
  angle pdb=" CB  MET A 732 "
        pdb=" CG  MET A 732 "
        pdb=" SD  MET A 732 "
      ideal   model   delta    sigma   weight residual
     112.70  122.65   -9.95 3.00e+00 1.11e-01 1.10e+01
  angle pdb=" N   MET B 525 "
        pdb=" CA  MET B 525 "
        pdb=" CB  MET B 525 "
      ideal   model   delta    sigma   weight residual
     110.12  114.72   -4.60 1.47e+00 4.63e-01 9.78e+00
  angle pdb=" CB  MET A1040 "
        pdb=" CG  MET A1040 "
        pdb=" SD  MET A1040 "
      ideal   model   delta    sigma   weight residual
     112.70  121.87   -9.17 3.00e+00 1.11e-01 9.33e+00
  angle pdb=" CB  LYS B 480 "
        pdb=" CG  LYS B 480 "
        pdb=" CD  LYS B 480 "
      ideal   model   delta    sigma   weight residual
     111.30  118.10   -6.80 2.30e+00 1.89e-01 8.75e+00
  ... (remaining 14323 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 5770
       17.98 -    35.97: 594
       35.97 -    53.95: 113
       53.95 -    71.93: 17
       71.93 -    89.91: 12
  Dihedral angle restraints: 6506
    sinusoidal: 2790
      harmonic: 3716
  Sorted by residual:
  dihedral pdb=" CA  LYS A 573 "
           pdb=" C   LYS A 573 "
           pdb=" N   TRP A 574 "
           pdb=" CA  TRP A 574 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.67  -18.33     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  MET B 326 "
           pdb=" C   MET B 326 "
           pdb=" N   SER B 327 "
           pdb=" CA  SER B 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.65  -17.35     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ASP A 646 "
           pdb=" CB  ASP A 646 "
           pdb=" CG  ASP A 646 "
           pdb=" OD1 ASP A 646 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.23   58.23     1      2.00e+01 2.50e-03 1.14e+01
  ... (remaining 6503 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 967
       0.033 -    0.067: 404
       0.067 -    0.100: 113
       0.100 -    0.134: 51
       0.134 -    0.167: 7
  Chirality restraints: 1542
  Sorted by residual:
  chirality pdb=" CA  LYS B 480 "
            pdb=" N   LYS B 480 "
            pdb=" C   LYS B 480 "
            pdb=" CB  LYS B 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.97e-01
  chirality pdb=" CA  GLN A 738 "
            pdb=" N   GLN A 738 "
            pdb=" C   GLN A 738 "
            pdb=" CB  GLN A 738 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.01e-01
  chirality pdb=" CA  THR A1053 "
            pdb=" N   THR A1053 "
            pdb=" C   THR A1053 "
            pdb=" CB  THR A1053 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.15 2.00e-01 2.50e+01 5.53e-01
  ... (remaining 1539 not shown)

  Planarity restraints: 1841
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 216 "   -0.040 5.00e-02 4.00e+02   6.09e-02 5.94e+00
        pdb=" N   PRO A 217 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 217 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 217 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 177 "    0.036 5.00e-02 4.00e+02   5.46e-02 4.77e+00
        pdb=" N   PRO A 178 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 178 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 178 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  56 "   -0.028 5.00e-02 4.00e+02   4.29e-02 2.94e+00
        pdb=" N   PRO A  57 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A  57 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  57 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1838 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1416
        2.76 -     3.29: 10300
        3.29 -     3.83: 17329
        3.83 -     4.36: 20116
        4.36 -     4.90: 34360
  Nonbonded interactions: 83521
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 540 "
            pdb=" NH2 ARG B 340 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OE2 GLU A 469 "
            pdb=" NH1 ARG B 481 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OH  TYR A 584 "
            pdb=" OD1 ASP A 608 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OD1 ASP B 540 "
            pdb=" NH2 ARG B 543 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" NZ  LYS A 440 "
            pdb=" OE1 GLU A 474 "
     model   vdw
     2.272 3.120
  ... (remaining 83516 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.060
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
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      :  0.003   0.050  10627  Z= 0.133
  Angle     :  0.647   9.949  14328  Z= 0.321
  Chirality :  0.043   0.167   1542
  Planarity :  0.004   0.061   1841
  Dihedral  : 14.944  89.912   4096
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.82 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.21 (0.24), residues: 1250
  helix:  0.84 (0.22), residues: 579
  sheet: -0.23 (0.44), residues: 143
  loop : -0.42 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 281 
 TYR   0.013   0.001   TYR B 556 
 PHE   0.024   0.001   PHE B 456 
 TRP   0.013   0.001   TRP A1051 
 HIS   0.005   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10627)
  covalent geometry    : angle       0.64654 (14328)
  hydrogen bonds       : bond        0.14668 (  485)
  hydrogen bonds       : angle       5.72227 ( 1416)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 GLU cc_start: 0.6322 (tm-30) cc_final: 0.5979 (tm-30)
REVERT: A  212 ASN cc_start: 0.8424 (p0) cc_final: 0.8185 (p0)
REVERT: A  267 LEU cc_start: 0.8422 (tt) cc_final: 0.8161 (tt)
REVERT: A  689 GLU cc_start: 0.6586 (tm-30) cc_final: 0.6259 (tm-30)
REVERT: A 1032 GLU cc_start: 0.6891 (mp0) cc_final: 0.6510 (mp0)
REVERT: A 1055 MET cc_start: 0.4148 (tmm) cc_final: 0.3831 (tmm)
REVERT: B  521 ILE cc_start: 0.6292 (mm) cc_final: 0.5200 (mm)
REVERT: B  578 ASP cc_start: 0.7625 (m-30) cc_final: 0.7368 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.1024
  time to fit residues: 35.0899
Evaluate side-chains
  201 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 123 optimal weight:    8.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
A 444 ASN
A 457 ASN
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.180852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.128222 restraints weight = 46145.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 5.53
r_work: 0.3383 rms_B_bonded: 5.16 restraints_weight: 2.0000
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3384
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3383 r_free = 0.3383    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3383
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  10627  Z= 0.236
  Angle     :  0.699   9.075  14328  Z= 0.362
  Chirality :  0.047   0.159   1542
  Planarity :  0.005   0.057   1841
  Dihedral  :  4.270  18.205   1385
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.14 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 10.03 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.08 (0.24), residues: 1250
  helix:  0.66 (0.21), residues: 591
  sheet: -0.99 (0.43), residues: 141
  loop : -0.48 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 481 
 TYR   0.033   0.002   TYR A 904 
 PHE   0.019   0.002   PHE A 909 
 TRP   0.014   0.002   TRP A 479 
 HIS   0.005   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 (10627)
  covalent geometry    : angle       0.69903 (14328)
  hydrogen bonds       : bond        0.04629 (  485)
  hydrogen bonds       : angle       4.40173 ( 1416)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 202
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7899 (mm-30)
REVERT: A  172 GLU cc_start: 0.6781 (tm-30) cc_final: 0.6574 (tm-30)
REVERT: A  689 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8018 (tm-30)
REVERT: A 1032 GLU cc_start: 0.7286 (mp0) cc_final: 0.7051 (mp0)
REVERT: B  508 TYR cc_start: 0.8277 (m-80) cc_final: 0.8071 (m-80)
REVERT: B  521 ILE cc_start: 0.6519 (mm) cc_final: 0.5910 (mm)
REVERT: B  525 MET cc_start: 0.8606 (mpp) cc_final: 0.8402 (mpp)
REVERT: B  578 ASP cc_start: 0.8003 (m-30) cc_final: 0.7571 (m-30)
  outliers start: 19
  outliers final: 14
  residues processed: 212
  average time/residue: 0.1035
  time to fit residues: 30.9868
Evaluate side-chains
  196 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 182
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 CYS
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 79 optimal weight:    0.6980
   chunk 120 optimal weight:    6.9990
   chunk 99 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 86 optimal weight:    0.0770
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 98 optimal weight:    7.9990
   chunk 104 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.8742

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

Flipped N/Q/H residues before XYZ refinement:
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 453 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.182928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.130107 restraints weight = 44038.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 5.13
r_work: 0.3441 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10627  Z= 0.129
  Angle     :  0.597  13.092  14328  Z= 0.305
  Chirality :  0.043   0.163   1542
  Planarity :  0.004   0.054   1841
  Dihedral  :  4.020  17.041   1385
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.34 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 12.79 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.13 (0.24), residues: 1250
  helix:  0.90 (0.21), residues: 595
  sheet: -1.11 (0.41), residues: 146
  loop : -0.40 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 741 
 TYR   0.012   0.001   TYR B 556 
 PHE   0.011   0.001   PHE A 667 
 TRP   0.015   0.001   TRP A 669 
 HIS   0.005   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10627)
  covalent geometry    : angle       0.59662 (14328)
  hydrogen bonds       : bond        0.03744 (  485)
  hydrogen bonds       : angle       4.11487 ( 1416)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 200
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7815 (mm)
REVERT: A  689 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7456 (tm-30)
REVERT: A  739 MET cc_start: 0.7209 (mmm) cc_final: 0.6988 (mmm)
REVERT: B  419 LYS cc_start: 0.7930 (mppt) cc_final: 0.7024 (mtmt)
REVERT: B  476 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6883 (mp0)
REVERT: B  578 ASP cc_start: 0.7982 (m-30) cc_final: 0.7554 (m-30)
  outliers start: 16
  outliers final: 9
  residues processed: 206
  average time/residue: 0.0945
  time to fit residues: 27.6874
Evaluate side-chains
  196 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 185
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  476 GLU
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 71 optimal weight:    0.0980
   chunk 82 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.183283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.133509 restraints weight = 53629.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 6.10
r_work: 0.3418 rms_B_bonded: 5.38 restraints_weight: 2.0000
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3419
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3419 r_free = 0.3419    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3419 r_free = 0.3419    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3419
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10627  Z= 0.117
  Angle     :  0.571   8.121  14328  Z= 0.293
  Chirality :  0.042   0.146   1542
  Planarity :  0.004   0.055   1841
  Dihedral  :  3.930  16.542   1385
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.50 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.00 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.27 (0.24), residues: 1250
  helix:  1.02 (0.21), residues: 597
  sheet: -1.02 (0.41), residues: 146
  loop : -0.34 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 281 
 TYR   0.012   0.001   TYR B 556 
 PHE   0.011   0.001   PHE A 667 
 TRP   0.013   0.001   TRP A 669 
 HIS   0.012   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10627)
  covalent geometry    : angle       0.57095 (14328)
  hydrogen bonds       : bond        0.03538 (  485)
  hydrogen bonds       : angle       3.95127 ( 1416)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 192
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7756 (pt0)
REVERT: A  252 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7834 (mm)
REVERT: A  263 GLU cc_start: 0.7767 (tp30) cc_final: 0.7550 (tm-30)
REVERT: A  265 TYR cc_start: 0.7143 (m-80) cc_final: 0.6716 (m-10)
REVERT: A  689 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7526 (tm-30)
REVERT: A  978 GLU cc_start: 0.8440 (mp0) cc_final: 0.7920 (pm20)
REVERT: B  381 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8369 (mt)
REVERT: B  419 LYS cc_start: 0.7998 (mppt) cc_final: 0.7214 (mmtp)
REVERT: B  476 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6875 (mt-10)
REVERT: B  489 GLU cc_start: 0.8808 (tp30) cc_final: 0.8336 (tp30)
REVERT: B  492 LYS cc_start: 0.8135 (mttt) cc_final: 0.7883 (mttt)
REVERT: B  578 ASP cc_start: 0.8116 (m-30) cc_final: 0.7704 (m-30)
  outliers start: 22
  outliers final: 16
  residues processed: 199
  average time/residue: 0.1011
  time to fit residues: 28.3260
Evaluate side-chains
  198 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 178
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  476 GLU
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  563 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 113 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9990
   chunk 117 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.178428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.126172 restraints weight = 49476.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 5.78
r_work: 0.3339 rms_B_bonded: 5.29 restraints_weight: 2.0000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3340
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3340
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  10627  Z= 0.231
  Angle     :  0.660   7.876  14328  Z= 0.341
  Chirality :  0.045   0.148   1542
  Planarity :  0.005   0.054   1841
  Dihedral  :  4.301  25.986   1385
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.30 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.61 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.19 (0.24), residues: 1250
  helix:  0.66 (0.21), residues: 605
  sheet: -1.40 (0.40), residues: 144
  loop : -0.55 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 401 
 TYR   0.015   0.002   TYR B 470 
 PHE   0.019   0.002   PHE A 980 
 TRP   0.014   0.002   TRP A 669 
 HIS   0.013   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (10627)
  covalent geometry    : angle       0.65958 (14328)
  hydrogen bonds       : bond        0.04437 (  485)
  hydrogen bonds       : angle       4.10993 ( 1416)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 185
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7266 (pm20)
REVERT: A  218 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7937 (pt0)
REVERT: A  263 GLU cc_start: 0.7952 (tp30) cc_final: 0.7712 (mt-10)
REVERT: A  689 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8006 (tm-30)
REVERT: A  710 GLU cc_start: 0.8039 (pp20) cc_final: 0.7821 (pt0)
REVERT: A  729 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8145 (mmtm)
REVERT: A  978 GLU cc_start: 0.8574 (mp0) cc_final: 0.8291 (pt0)
REVERT: B  419 LYS cc_start: 0.8089 (mppt) cc_final: 0.7351 (mmtp)
REVERT: B  492 LYS cc_start: 0.8238 (mttt) cc_final: 0.7961 (mttt)
  outliers start: 28
  outliers final: 20
  residues processed: 199
  average time/residue: 0.1013
  time to fit residues: 28.6146
Evaluate side-chains
  198 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 176
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  563 MET
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 99 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 110 optimal weight:   20.0000
   chunk 123 optimal weight:    3.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.178756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.128983 restraints weight = 31900.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 3.93
r_work: 0.3410 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3412
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3412 r_free = 0.3412    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3412 r_free = 0.3412    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3412
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10627  Z= 0.183
  Angle     :  0.645  14.577  14328  Z= 0.327
  Chirality :  0.044   0.190   1542
  Planarity :  0.004   0.055   1841
  Dihedral  :  4.224  19.317   1385
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.14 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.47 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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: -0.13 (0.24), residues: 1250
  helix:  0.67 (0.21), residues: 604
  sheet: -1.34 (0.42), residues: 138
  loop : -0.50 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 281 
 TYR   0.031   0.001   TYR A 904 
 PHE   0.013   0.002   PHE A 734 
 TRP   0.015   0.001   TRP A 669 
 HIS   0.010   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (10627)
  covalent geometry    : angle       0.64520 (14328)
  hydrogen bonds       : bond        0.04074 (  485)
  hydrogen bonds       : angle       4.04162 ( 1416)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 190
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7256 (pm20)
REVERT: A  172 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6066 (tp30)
REVERT: A  218 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7826 (pt0)
REVERT: A  252 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7858 (mm)
REVERT: A  282 MET cc_start: 0.7051 (tpp) cc_final: 0.6746 (tpt)
REVERT: A  689 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7655 (tm-30)
REVERT: A  794 PHE cc_start: 0.7922 (p90) cc_final: 0.7480 (p90)
REVERT: B  348 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8188 (ttm170)
REVERT: B  419 LYS cc_start: 0.8087 (mppt) cc_final: 0.7685 (mtmm)
  outliers start: 30
  outliers final: 17
  residues processed: 203
  average time/residue: 0.1056
  time to fit residues: 30.5946
Evaluate side-chains
  202 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  525 MET
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  563 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 110 optimal weight:   20.0000
   chunk 106 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 104 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.180379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.133281 restraints weight = 28131.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 3.81
r_work: 0.3460 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3464
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3464 r_free = 0.3464    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10627  Z= 0.124
  Angle     :  0.604  10.300  14328  Z= 0.305
  Chirality :  0.042   0.171   1542
  Planarity :  0.004   0.056   1841
  Dihedral  :  4.067  17.125   1385
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.14 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.77 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.13 (0.24), residues: 1250
  helix:  0.89 (0.21), residues: 604
  sheet: -1.17 (0.42), residues: 138
  loop : -0.38 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 281 
 TYR   0.016   0.001   TYR A 265 
 PHE   0.011   0.001   PHE A 667 
 TRP   0.015   0.001   TRP A 669 
 HIS   0.005   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (10627)
  covalent geometry    : angle       0.60406 (14328)
  hydrogen bonds       : bond        0.03546 (  485)
  hydrogen bonds       : angle       3.89611 ( 1416)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 191
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7231 (pm20)
REVERT: A  218 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7793 (pt0)
REVERT: A  252 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7750 (mm)
REVERT: A  263 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7223 (tt0)
REVERT: A  689 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7460 (tm-30)
REVERT: A  729 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8038 (mmmt)
REVERT: A  739 MET cc_start: 0.6521 (mmm) cc_final: 0.6258 (mmm)
REVERT: B  381 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8464 (mt)
REVERT: B  489 GLU cc_start: 0.8506 (tp30) cc_final: 0.8178 (tp30)
  outliers start: 21
  outliers final: 17
  residues processed: 200
  average time/residue: 0.1021
  time to fit residues: 29.2222
Evaluate side-chains
  205 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 184
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  525 MET
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  563 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 57 optimal weight:    0.3980
   chunk 46 optimal weight:    5.9990
   chunk 106 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 119 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 180 HIS
A 213 HIS
A 450 HIS
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.178926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.126037 restraints weight = 45546.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 5.28
r_work: 0.3387 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3387
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10627  Z= 0.161
  Angle     :  0.638   9.521  14328  Z= 0.325
  Chirality :  0.044   0.165   1542
  Planarity :  0.004   0.057   1841
  Dihedral  :  4.147  17.626   1385
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.82 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.25 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.05 (0.24), residues: 1250
  helix:  0.78 (0.21), residues: 603
  sheet: -1.16 (0.43), residues: 138
  loop : -0.38 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 543 
 TYR   0.021   0.001   TYR A 265 
 PHE   0.013   0.002   PHE A 667 
 TRP   0.014   0.001   TRP A 669 
 HIS   0.008   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (10627)
  covalent geometry    : angle       0.63812 (14328)
  hydrogen bonds       : bond        0.03861 (  485)
  hydrogen bonds       : angle       3.94246 ( 1416)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 186
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 LYS cc_start: 0.7959 (tmtt) cc_final: 0.7568 (tmtt)
REVERT: A  110 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7251 (pm20)
REVERT: A  218 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7842 (pm20)
REVERT: A  252 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7790 (mm)
REVERT: A  263 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7544 (tt0)
REVERT: A  689 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7721 (tm-30)
REVERT: A  710 GLU cc_start: 0.8064 (pp20) cc_final: 0.7853 (pt0)
REVERT: A  729 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8059 (mmmt)
REVERT: A  739 MET cc_start: 0.6751 (mmm) cc_final: 0.6416 (mmm)
REVERT: A  794 PHE cc_start: 0.7955 (p90) cc_final: 0.7479 (p90)
REVERT: B  381 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8524 (mt)
REVERT: B  480 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8304 (mmtt)
  outliers start: 29
  outliers final: 23
  residues processed: 196
  average time/residue: 0.1021
  time to fit residues: 28.5809
Evaluate side-chains
  210 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 183
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  450 HIS
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain A residue 1055 MET
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  525 MET
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  563 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 115 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 74 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 20 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 89 optimal weight:    0.4980
   chunk 90 optimal weight:    2.9990
   chunk 117 optimal weight:   30.0000
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 450 HIS
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.180160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.127924 restraints weight = 47364.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 5.45
r_work: 0.3398 rms_B_bonded: 5.12 restraints_weight: 2.0000
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3401
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3401
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10627  Z= 0.127
  Angle     :  0.619   9.760  14328  Z= 0.313
  Chirality :  0.043   0.168   1542
  Planarity :  0.004   0.056   1841
  Dihedral  :  4.096  17.065   1385
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.38 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.94 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.17 (0.24), residues: 1250
  helix:  0.89 (0.21), residues: 603
  sheet: -1.09 (0.43), residues: 138
  loop : -0.35 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 543 
 TYR   0.021   0.001   TYR A 265 
 PHE   0.011   0.001   PHE A 667 
 TRP   0.015   0.001   TRP A 669 
 HIS   0.012   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10627)
  covalent geometry    : angle       0.61910 (14328)
  hydrogen bonds       : bond        0.03595 (  485)
  hydrogen bonds       : angle       3.87044 ( 1416)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 187
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7697 (tmtt)
REVERT: A  110 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7221 (pm20)
REVERT: A  218 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7816 (pm20)
REVERT: A  252 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7747 (mm)
REVERT: A  263 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7543 (tt0)
REVERT: A  282 MET cc_start: 0.7190 (tpp) cc_final: 0.6924 (tpt)
REVERT: A  689 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7560 (tm-30)
REVERT: A  729 LYS cc_start: 0.8394 (mmmt) cc_final: 0.8015 (mmmt)
REVERT: A  739 MET cc_start: 0.6744 (mmm) cc_final: 0.6434 (mmm)
REVERT: A  794 PHE cc_start: 0.7941 (p90) cc_final: 0.7474 (p90)
REVERT: B  381 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8477 (mt)
  outliers start: 29
  outliers final: 21
  residues processed: 199
  average time/residue: 0.0956
  time to fit residues: 27.2610
Evaluate side-chains
  209 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue  959 ASP
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain A residue 1055 MET
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  498 CYS
Chi-restraints excluded: chain B residue  525 MET
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  563 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0980
   chunk 1 optimal weight:   10.0000
   chunk 91 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0270
   chunk 19 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.181579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.129697 restraints weight = 49432.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 5.62
r_work: 0.3427 rms_B_bonded: 5.20 restraints_weight: 2.0000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3428
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3428 r_free = 0.3428    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3428
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10627  Z= 0.114
  Angle     :  0.605   9.828  14328  Z= 0.304
  Chirality :  0.042   0.165   1542
  Planarity :  0.004   0.057   1841
  Dihedral  :  3.976  16.169   1385
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.90 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.55 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.24 (0.24), residues: 1250
  helix:  0.99 (0.21), residues: 604
  sheet: -1.00 (0.43), residues: 144
  loop : -0.37 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 543 
 TYR   0.018   0.001   TYR A 265 
 PHE   0.012   0.001   PHE A 960 
 TRP   0.013   0.001   TRP A 669 
 HIS   0.005   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10627)
  covalent geometry    : angle       0.60537 (14328)
  hydrogen bonds       : bond        0.03326 (  485)
  hydrogen bonds       : angle       3.76808 ( 1416)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 193
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7255 (pm20)
REVERT: A  218 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7822 (pm20)
REVERT: A  252 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7688 (mm)
REVERT: A  263 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7517 (tt0)
REVERT: A  528 LYS cc_start: 0.8724 (ptpp) cc_final: 0.8455 (mtpp)
REVERT: A  689 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7519 (tm-30)
REVERT: A  729 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8122 (mmmt)
REVERT: A  739 MET cc_start: 0.6674 (mmm) cc_final: 0.6373 (mmm)
REVERT: A  741 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7600 (mmm-85)
REVERT: B  419 LYS cc_start: 0.8208 (mppt) cc_final: 0.7407 (mmtp)
REVERT: B  564 ASN cc_start: 0.7961 (m-40) cc_final: 0.7711 (m110)
  outliers start: 21
  outliers final: 15
  residues processed: 201
  average time/residue: 0.0927
  time to fit residues: 26.9266
Evaluate side-chains
  204 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 186
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  193 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  218 GLU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain A residue  856 THR
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1029 ASP
Chi-restraints excluded: chain B residue  326 MET
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  464 ASP
Chi-restraints excluded: chain B residue  525 MET
Chi-restraints excluded: chain B residue  531 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 111 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0270
   chunk 80 optimal weight:    7.9990
   chunk 47 optimal weight:    0.7980
   chunk 112 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
A 450 HIS
** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.181195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.129190 restraints weight = 44122.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 5.06
r_work: 0.3443 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3446
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3446 r_free = 0.3446    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3446
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10627  Z= 0.121
  Angle     :  0.613  10.025  14328  Z= 0.309
  Chirality :  0.042   0.160   1542
  Planarity :  0.004   0.057   1841
  Dihedral  :  3.965  16.272   1385
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.14 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.24 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.29 (0.24), residues: 1250
  helix:  1.01 (0.21), residues: 604
  sheet: -0.93 (0.43), residues: 144
  loop : -0.32 (0.29), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 543 
 TYR   0.017   0.001   TYR A 265 
 PHE   0.012   0.001   PHE A 960 
 TRP   0.013   0.001   TRP A 669 
 HIS   0.005   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10627)
  covalent geometry    : angle       0.61309 (14328)
  hydrogen bonds       : bond        0.03400 (  485)
  hydrogen bonds       : angle       3.75553 ( 1416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3206.90 seconds
wall clock time: 55 minutes 20.88 seconds (3320.88 seconds total)