Starting phenix.real_space_refine
on Wed Feb  4 12:05:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7myo_24082/02_2026/7myo_24082.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7myo_24082/02_2026/7myo_24082.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7myo_24082/02_2026/7myo_24082.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7myo_24082/02_2026/7myo_24082.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7myo_24082/02_2026/7myo_24082.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7myo_24082/02_2026/7myo_24082.cif"
  }
  resolution = 2.92
  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: 5
    Type Number    sf(0)   Gaussians
     S      77      5.16       5
     C    6763      2.51       5
     N    1848      2.21       5
     O    1943      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10634
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 2412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2412
          Classifications: {'peptide': 286}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 281}
    Chain: "A"
      Number of atoms: 8192
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 992, 8107
          Classifications: {'peptide': 992}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 945}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 992, 8107
          Classifications: {'peptide': 992}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 945}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 8193
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'1LT': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 9
    residue:
      pdb=" N  AARG A 617 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 617 " occ=0.50
    residue:
      pdb=" N  ALYS A 621 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS A 621 " occ=0.50
    residue:
      pdb=" N  AARG A 662 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 662 " occ=0.50
    residue:
      pdb=" N  AARG A 899 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 899 " occ=0.50
    residue:
      pdb=" N  AARG A 951 " occ=0.63
      ... (20 atoms not shown)
      pdb=" NH2BARG A 951 " occ=0.37
    residue:
      pdb=" N  AVAL A 952 " occ=0.63
      ... (12 atoms not shown)
      pdb=" CG2BVAL A 952 " occ=0.37
    residue:
      pdb=" N  APRO A 953 " occ=0.63
      ... (12 atoms not shown)
      pdb=" CD BPRO A 953 " occ=0.37
    residue:
      pdb=" N  APHE A 954 " occ=0.63
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 954 " occ=0.37
    residue:
      pdb=" N  AVAL A 955 " occ=0.63
      ... (12 atoms not shown)
      pdb=" CG2BVAL A 955 " occ=0.37
  Time building chain proxies: 3.60, per 1000 atoms: 0.34
  Number of scatterers: 10634
  At special positions: 0
  Unit cell: (89.87, 108.68, 135.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      77     16.00
     F       3      9.00
     O    1943      8.00
     N    1848      7.00
     C    6763      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 753.3 milliseconds
  

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2466

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 10 sheets defined
      50.5% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'B' and resid 339 through 348
    Processing helix  chain 'B' and resid 385 through 389
      removed outlier: 4.091A  pdb=" N   GLY B 388 " --> pdb=" O   HIS B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 411
    Processing helix  chain 'B' and resid 432 through 436
    Processing helix  chain 'B' and resid 441 through 506
      removed outlier: 3.595A  pdb=" N   VAL B 445 " --> pdb=" O   ASN B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 515
      removed outlier: 3.799A  pdb=" N   PHE B 512 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 588
      removed outlier: 3.927A  pdb=" N   LEU B 531 " --> pdb=" O   ASN B 527 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS B 532 " --> pdb=" O   TYR B 528 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASP B 548 " --> pdb=" O   ARG B 544 " (cutoff:3.500A)
      Proline residue:  B 568  - end of helix
    Processing helix  chain 'B' and resid 593 through 599
      removed outlier: 3.915A  pdb=" N   TRP B 597 " --> pdb=" O   LYS B 593 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU B 598 " --> pdb=" O   LEU B 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 56
      removed outlier: 3.605A  pdb=" N   HIS A  47 " --> pdb=" O   ILE A  43 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   GLU A  48 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 122
      removed outlier: 3.815A  pdb=" N   LYS A 111 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 131
      removed outlier: 3.990A  pdb=" N   PHE A 128 " --> pdb=" O   PRO A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 155
      removed outlier: 3.541A  pdb=" N   GLN A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   LEU A 144 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ASN A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   VAL A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 167
    Processing helix  chain 'A' and resid 178 through 183
      removed outlier: 3.657A  pdb=" N   ASN A 183 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 229
      removed outlier: 3.785A  pdb=" N   VAL A 220 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 248
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 290 through 297
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 326 through 330
      removed outlier: 3.690A  pdb=" N   VAL A 329 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 488 through 502
      removed outlier: 3.863A  pdb=" N   ILE A 492 " --> pdb=" O   ASP A 488 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL A 500 " --> pdb=" O   ALA A 496 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   SER A 501 " --> pdb=" O   ASN A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 536
      removed outlier: 3.824A  pdb=" N   LYS A 528 " --> pdb=" O   ARG A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 554
    Processing helix  chain 'A' and resid 564 through 571
    Processing helix  chain 'A' and resid 577 through 589
      removed outlier: 3.620A  pdb=" N   ALA A 581 " --> pdb=" O   ARG A 577 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ASP A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 600 through 603
      removed outlier: 4.119A  pdb=" N   ASP A 603 " --> pdb=" O   GLU A 600 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 600 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 642
      removed outlier: 3.902A  pdb=" N   LYS A 640 " --> pdb=" O   VAL A 636 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   TYR A 641 " --> pdb=" O   GLN A 637 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU A 642 " --> pdb=" O   VAL A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 658
    Processing helix  chain 'A' and resid 660 through 673
    Processing helix  chain 'A' and resid 680 through 695
    Processing helix  chain 'A' and resid 697 through 721
      removed outlier: 3.807A  pdb=" N   HIS A 701 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 740
    Processing helix  chain 'A' and resid 741 through 746
    Processing helix  chain 'A' and resid 747 through 749
      No H-bonds generated for 'chain 'A' and resid 747 through 749'
    Processing helix  chain 'A' and resid 787 through 793
      removed outlier: 4.438A  pdb=" N   GLU A 791 " --> pdb=" O   ILE A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 828
    Processing helix  chain 'A' and resid 857 through 867
    Processing helix  chain 'A' and resid 875 through 885
    Processing helix  chain 'A' and resid 886 through 888
      No H-bonds generated for 'chain 'A' and resid 886 through 888'
    Processing helix  chain 'A' and resid 889 through 911
      removed outlier: 4.451A  pdb=" N   VAL A 906 " --> pdb=" O   ALA A 902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 957 through 965
      removed outlier: 3.521A  pdb=" N   LEU A 961 " --> pdb=" O   THR A 957 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER A 965 " --> pdb=" O   LEU A 961 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 993
      removed outlier: 4.092A  pdb=" N   GLU A 978 " --> pdb=" O   THR A 974 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ARG A 979 " --> pdb=" O   ARG A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1004
      removed outlier: 3.696A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1019 through 1026
    Processing helix  chain 'A' and resid 1031 through 1045
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 355
    Processing sheet with id=AA2, first strand: chain 'B' and resid 373 through 374
    Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 36
      removed outlier: 3.615A  pdb=" N   VAL A  32 " --> pdb=" O   CYS A  24 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   LEU A  99 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   GLU A  23 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   VAL A 101 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   LEU A  25 " --> pdb=" O   VAL A 101 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   PHE A  98 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   VAL A  73 " --> pdb=" O   PHE A  98 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   PHE A  70 " --> pdb=" O   PHE A  82 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   SER A  72 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 212
      removed outlier: 8.429A  pdb=" N   LEU A 285 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   VAL A 193 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 7.465A  pdb=" N   LEU A 287 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS A 253 " --> pdb=" O   MET A 286 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   LEU A 252 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 392
      removed outlier: 6.393A  pdb=" N   TRP A 383 " --> pdb=" O   CYS A 340 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   CYS A 340 " --> pdb=" O   TRP A 383 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   ALA A 341 " --> pdb=" O   CYS A 472 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   CYS A 472 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.516A  pdb=" N   VAL A 409 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   LYS A 353 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 365 through 366
      removed outlier: 6.430A  pdb=" N   SER A 408 " --> pdb=" O   PRO A 421 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 752 through 753
      removed outlier: 5.885A  pdb=" N   HIS A 759 " --> pdb=" O   SER A 753 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 770 through 771
    Processing sheet with id=AB1, first strand: chain 'A' and resid 854 through 856

    499 hydrogen bonds defined for protein.
    1437 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.21

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1774
        1.32 -     1.44: 2816
        1.44 -     1.56: 6146
        1.56 -     1.69: 2
        1.69 -     1.81: 121
  Bond restraints: 10859
  Sorted by residual:
  bond pdb=" C3  1LT A1101 "
       pdb=" N1  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.391  1.485 -0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" C2  1LT A1101 "
       pdb=" N1  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.368  1.458 -0.090 2.00e-02 2.50e+03 2.04e+01
  bond pdb=" C3  1LT A1101 "
       pdb=" N2  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.348  1.435 -0.087 2.00e-02 2.50e+03 1.87e+01
  bond pdb=" N   1LT A1101 "
       pdb=" C1  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.368  1.445 -0.077 2.00e-02 2.50e+03 1.47e+01
  bond pdb=" C7  1LT A1101 "
       pdb=" N2  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.444  1.520 -0.076 2.00e-02 2.50e+03 1.43e+01
  ... (remaining 10854 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 14279
        2.57 -     5.14: 306
        5.14 -     7.71: 57
        7.71 -    10.28: 5
       10.28 -    12.86: 4
  Bond angle restraints: 14651
  Sorted by residual:
  angle pdb=" N   ASP A1017 "
        pdb=" CA  ASP A1017 "
        pdb=" C   ASP A1017 "
      ideal   model   delta    sigma   weight residual
     114.31  108.20    6.11 1.29e+00 6.01e-01 2.25e+01
  angle pdb=" C   ASP A 939 "
        pdb=" N   HIS A 940 "
        pdb=" CA  HIS A 940 "
      ideal   model   delta    sigma   weight residual
     121.54  129.94   -8.40 1.91e+00 2.74e-01 1.93e+01
  angle pdb=" N   GLU B 537 "
        pdb=" CA  GLU B 537 "
        pdb=" CB  GLU B 537 "
      ideal   model   delta    sigma   weight residual
     110.30  117.00   -6.70 1.54e+00 4.22e-01 1.90e+01
  angle pdb=" CB  MET A1040 "
        pdb=" CG  MET A1040 "
        pdb=" SD  MET A1040 "
      ideal   model   delta    sigma   weight residual
     112.70  125.56  -12.86 3.00e+00 1.11e-01 1.84e+01
  angle pdb=" CG1 ILE A 211 "
        pdb=" CB  ILE A 211 "
        pdb=" CG2 ILE A 211 "
      ideal   model   delta    sigma   weight residual
     110.70   99.90   10.80 3.00e+00 1.11e-01 1.30e+01
  ... (remaining 14646 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 5886
       17.47 -    34.95: 618
       34.95 -    52.42: 113
       52.42 -    69.89: 32
       69.89 -    87.36: 13
  Dihedral angle restraints: 6662
    sinusoidal: 2859
      harmonic: 3803
  Sorted by residual:
  dihedral pdb=" CA  LEU A 209 "
           pdb=" C   LEU A 209 "
           pdb=" N   LYS A 210 "
           pdb=" CA  LYS A 210 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.50  -26.50     0      5.00e+00 4.00e-02 2.81e+01
  dihedral pdb=" CA  PHE B 512 "
           pdb=" C   PHE B 512 "
           pdb=" N   LYS B 513 "
           pdb=" CA  LYS B 513 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.45   20.55     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  LEU A 262 "
           pdb=" C   LEU A 262 "
           pdb=" N   GLU A 263 "
           pdb=" CA  GLU A 263 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.54  -18.46     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 6659 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1062
       0.044 -    0.088: 374
       0.088 -    0.132: 117
       0.132 -    0.175: 19
       0.175 -    0.219: 9
  Chirality restraints: 1581
  Sorted by residual:
  chirality pdb=" CB  ILE A 921 "
            pdb=" CA  ILE A 921 "
            pdb=" CG1 ILE A 921 "
            pdb=" CG2 ILE A 921 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  ASN A 202 "
            pdb=" N   ASN A 202 "
            pdb=" C   ASN A 202 "
            pdb=" CB  ASN A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.93e-01
  chirality pdb=" CG  LEU A 267 "
            pdb=" CB  LEU A 267 "
            pdb=" CD1 LEU A 267 "
            pdb=" CD2 LEU A 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.79    0.20 2.00e-01 2.50e+01 9.71e-01
  ... (remaining 1578 not shown)

  Planarity restraints: 1883
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 426 "    0.082 5.00e-02 4.00e+02   1.24e-01 2.44e+01
        pdb=" N   PRO B 427 "   -0.214 5.00e-02 4.00e+02
        pdb=" CA  PRO B 427 "    0.067 5.00e-02 4.00e+02
        pdb=" CD  PRO B 427 "    0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 177 "   -0.076 5.00e-02 4.00e+02   1.15e-01 2.11e+01
        pdb=" N   PRO A 178 "    0.198 5.00e-02 4.00e+02
        pdb=" CA  PRO A 178 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO A 178 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 457 "   -0.069 5.00e-02 4.00e+02   1.04e-01 1.72e+01
        pdb=" N   PRO A 458 "    0.179 5.00e-02 4.00e+02
        pdb=" CA  PRO A 458 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 458 "   -0.056 5.00e-02 4.00e+02
  ... (remaining 1880 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1491
        2.76 -     3.29: 10714
        3.29 -     3.83: 18393
        3.83 -     4.36: 21335
        4.36 -     4.90: 35211
  Nonbonded interactions: 87144
  Sorted by model distance:
  nonbonded pdb=" O   TYR A1038 "
            pdb=" OE1 GLN A1042 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OH  TYR A 988 "
            pdb=" O   LEU A1026 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OG  SER A 499 "
            pdb=" OE1 GLN A 582 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   ASP A 895 "
            pdb=" OG1 THR A 898 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OE2 GLU B 332 "
            pdb=" OH  TYR B 431 "
     model   vdw
     2.268 3.040
  ... (remaining 87139 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=0.37 max=1.00 mean=0.99
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:             0.450
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.170
  Find NCS groups from input model:        0.030
  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:5.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.094  10859  Z= 0.224
  Angle     :  0.894  12.856  14651  Z= 0.455
  Chirality :  0.051   0.219   1581
  Planarity :  0.008   0.124   1883
  Dihedral  : 15.195  87.363   4196
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  0.85 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.22), residues: 1281
  helix: -0.71 (0.19), residues: 593
  sheet: -1.80 (0.43), residues: 137
  loop : -1.73 (0.26), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 115 
 TYR   0.031   0.002   TYR A 165 
 PHE   0.035   0.003   PHE A 937 
 TRP   0.059   0.003   TRP B 335 
 HIS   0.017   0.001   HIS A 940 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 (10859)
  covalent geometry    : angle       0.89438 (14651)
  hydrogen bonds       : bond        0.15595 (  495)
  hydrogen bonds       : angle       6.51487 ( 1437)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 305
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  526 ASN cc_start: 0.7934 (p0) cc_final: 0.7636 (p0)
REVERT: A  988 TYR cc_start: 0.5782 (t80) cc_final: 0.5575 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 305
  average time/residue: 0.4728
  time to fit residues: 156.3075
Evaluate side-chains
  210 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 123 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
B 407 HIS
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 591 GLN
A 160 HIS
A 426 ASN
A 661 GLN
A 701 HIS
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 785 ASN
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.222250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.183056 restraints weight = 45511.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.4366 rms_B_bonded: 6.08
r_work: 0.4148 rms_B_bonded: 5.63 restraints_weight: 2.0000
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4181 r_free = 0.4181    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4179 r_free = 0.4179    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4179
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6868
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10859  Z= 0.160
  Angle     :  0.760  11.810  14651  Z= 0.380
  Chirality :  0.045   0.173   1581
  Planarity :  0.006   0.087   1883
  Dihedral  :  6.210  70.611   1437
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.12 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.23), residues: 1281
  helix:  0.14 (0.20), residues: 605
  sheet: -1.80 (0.43), residues: 142
  loop : -1.70 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 141 
 TYR   0.021   0.002   TYR A 432 
 PHE   0.040   0.002   PHE A 667 
 TRP   0.021   0.002   TRP A 780 
 HIS   0.012   0.001   HIS A 940 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (10859)
  covalent geometry    : angle       0.75954 (14651)
  hydrogen bonds       : bond        0.04356 (  495)
  hydrogen bonds       : angle       4.93071 ( 1437)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 240
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: B  479 MET cc_start: 0.7570 (pp-130) cc_final: 0.7259 (pp-130)
REVERT: A  164 MET cc_start: 0.7795 (mpp) cc_final: 0.6876 (mpt)
REVERT: A  330 ILE cc_start: 0.6195 (mt) cc_final: 0.5904 (mt)
REVERT: A  391 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7614 (tp)
REVERT: A  427 ILE cc_start: 0.8514 (mp) cc_final: 0.8126 (mt)
REVERT: A  563 GLU cc_start: 0.6716 (tp30) cc_final: 0.6015 (tp30)
REVERT: A  812 LEU cc_start: 0.7684 (tp) cc_final: 0.7387 (tp)
REVERT: A  979 ARG cc_start: 0.7781 (mtp180) cc_final: 0.7421 (tpt-90)
REVERT: A 1000 ASN cc_start: 0.7209 (t0) cc_final: 0.6513 (m-40)
REVERT: A 1039 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5986 (m-10)
  outliers start: 24
  outliers final: 6
  residues processed: 251
  average time/residue: 0.4112
  time to fit residues: 113.4593
Evaluate side-chains
  225 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 217
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  732 MET
Chi-restraints excluded: chain A residue  840 SER
Chi-restraints excluded: chain A residue 1039 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 71 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 90 optimal weight:    0.5980
   chunk 115 optimal weight:    0.7980
   chunk 99 optimal weight:    5.9990
   chunk 100 optimal weight:    0.7980
   chunk 92 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0370
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 499 GLN
A  59 HIS
A 202 ASN
** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 HIS
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.221118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.182200 restraints weight = 47602.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.4363 rms_B_bonded: 5.76
r_work: 0.4140 rms_B_bonded: 5.58 restraints_weight: 2.0000
r_work (final): 0.4140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4171 r_free = 0.4171    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4171 r_free = 0.4171    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6842
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10859  Z= 0.139
  Angle     :  0.719  10.526  14651  Z= 0.358
  Chirality :  0.044   0.293   1581
  Planarity :  0.005   0.074   1883
  Dihedral  :  5.912  67.199   1437
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.07 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.99 (0.23), residues: 1281
  helix:  0.43 (0.21), residues: 601
  sheet: -1.80 (0.42), residues: 142
  loop : -1.54 (0.27), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 141 
 TYR   0.022   0.002   TYR A 985 
 PHE   0.045   0.002   PHE A 667 
 TRP   0.024   0.001   TRP B 333 
 HIS   0.010   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (10859)
  covalent geometry    : angle       0.71949 (14651)
  hydrogen bonds       : bond        0.03874 (  495)
  hydrogen bonds       : angle       4.68030 ( 1437)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 229
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: B  367 ASP cc_start: 0.6179 (m-30) cc_final: 0.5962 (m-30)
REVERT: B  420 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6258 (mm)
REVERT: B  479 MET cc_start: 0.7321 (pp-130) cc_final: 0.6943 (pp-130)
REVERT: B  499 GLN cc_start: 0.7041 (tm130) cc_final: 0.6699 (tm130)
REVERT: B  537 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7611 (pm20)
REVERT: B  563 MET cc_start: 0.6202 (ppp) cc_final: 0.4367 (mtm)
REVERT: A   58 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6283 (mm)
REVERT: A  164 MET cc_start: 0.7601 (mpp) cc_final: 0.6763 (mpp)
REVERT: A  330 ILE cc_start: 0.6356 (mt) cc_final: 0.6048 (mt)
REVERT: A  427 ILE cc_start: 0.8507 (mp) cc_final: 0.8169 (mt)
REVERT: A  563 GLU cc_start: 0.6648 (tp30) cc_final: 0.5745 (tp30)
REVERT: A  760 GLN cc_start: 0.8054 (pt0) cc_final: 0.7586 (pt0)
REVERT: A  766 LEU cc_start: 0.8133 (pt) cc_final: 0.7767 (mm)
REVERT: A  812 LEU cc_start: 0.7594 (tp) cc_final: 0.7368 (tp)
REVERT: A  833 MET cc_start: 0.6343 (ptm) cc_final: 0.5934 (ptt)
REVERT: A  979 ARG cc_start: 0.7838 (mtp180) cc_final: 0.7435 (tpt-90)
REVERT: A 1000 ASN cc_start: 0.7073 (t0) cc_final: 0.6514 (m-40)
  outliers start: 33
  outliers final: 11
  residues processed: 242
  average time/residue: 0.3995
  time to fit residues: 106.0400
Evaluate side-chains
  220 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 206
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  430 LYS
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain B residue  540 ASP
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  732 MET
Chi-restraints excluded: chain A residue  840 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 116 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 202 ASN
** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 634 GLN
A 701 HIS
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 749 GLN
A 815 GLN
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.215831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.175724 restraints weight = 48725.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.4322 rms_B_bonded: 5.85
r_work: 0.4085 rms_B_bonded: 5.75 restraints_weight: 2.0000
r_work (final): 0.4085
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4091 r_free = 0.4091    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4091 r_free = 0.4091    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  10859  Z= 0.170
  Angle     :  0.726  10.188  14651  Z= 0.364
  Chirality :  0.045   0.278   1581
  Planarity :  0.005   0.069   1883
  Dihedral  :  5.831  64.790   1437
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 22.18 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.23), residues: 1281
  helix:  0.43 (0.21), residues: 611
  sheet: -1.86 (0.42), residues: 142
  loop : -1.60 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 141 
 TYR   0.031   0.002   TYR A 988 
 PHE   0.042   0.002   PHE A 667 
 TRP   0.027   0.002   TRP B 333 
 HIS   0.025   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (10859)
  covalent geometry    : angle       0.72645 (14651)
  hydrogen bonds       : bond        0.03815 (  495)
  hydrogen bonds       : angle       4.65087 ( 1437)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 235
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  420 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6261 (mm)
REVERT: B  422 VAL cc_start: 0.5958 (OUTLIER) cc_final: 0.5637 (t)
REVERT: B  479 MET cc_start: 0.7511 (pp-130) cc_final: 0.7114 (pp-130)
REVERT: B  534 ARG cc_start: 0.7677 (tpt-90) cc_final: 0.7377 (tpt-90)
REVERT: B  537 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7691 (pm20)
REVERT: A   58 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6353 (mm)
REVERT: A  318 MET cc_start: 0.5015 (ttt) cc_final: 0.4778 (mtm)
REVERT: A  427 ILE cc_start: 0.8756 (mp) cc_final: 0.8543 (mp)
REVERT: A  760 GLN cc_start: 0.8019 (pt0) cc_final: 0.7512 (pt0)
REVERT: A  979 ARG cc_start: 0.7914 (mtp180) cc_final: 0.7472 (tpt-90)
REVERT: A 1000 ASN cc_start: 0.7099 (t0) cc_final: 0.6466 (m-40)
REVERT: A 1039 PHE cc_start: 0.6351 (m-80) cc_final: 0.5951 (m-80)
  outliers start: 31
  outliers final: 15
  residues processed: 248
  average time/residue: 0.4331
  time to fit residues: 117.6796
Evaluate side-chains
  238 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 219
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  322 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  430 LYS
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain B residue  540 ASP
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  891 ASP
Chi-restraints excluded: chain A residue  957 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 115 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 108 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 46 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 121 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 202 ASN
** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 993 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.213935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.172938 restraints weight = 55298.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.4271 rms_B_bonded: 6.51
r_work: 0.4040 rms_B_bonded: 5.93 restraints_weight: 2.0000
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4055
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4055 r_free = 0.4055    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4055 r_free = 0.4055    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4055
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10859  Z= 0.170
  Angle     :  0.741  10.201  14651  Z= 0.369
  Chirality :  0.046   0.298   1581
  Planarity :  0.005   0.066   1883
  Dihedral  :  5.738  60.774   1437
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 17.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 23.79 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.23), residues: 1281
  helix:  0.44 (0.21), residues: 612
  sheet: -1.93 (0.41), residues: 142
  loop : -1.54 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 141 
 TYR   0.014   0.002   TYR A 988 
 PHE   0.041   0.002   PHE A 667 
 TRP   0.020   0.002   TRP A 552 
 HIS   0.006   0.001   HIS A 940 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (10859)
  covalent geometry    : angle       0.74129 (14651)
  hydrogen bonds       : bond        0.03733 (  495)
  hydrogen bonds       : angle       4.62643 ( 1437)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 240
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  367 ASP cc_start: 0.6421 (m-30) cc_final: 0.6200 (m-30)
REVERT: B  383 ILE cc_start: 0.7812 (pt) cc_final: 0.7599 (mp)
REVERT: B  422 VAL cc_start: 0.5879 (OUTLIER) cc_final: 0.5584 (t)
REVERT: B  479 MET cc_start: 0.7410 (pp-130) cc_final: 0.6990 (pp-130)
REVERT: B  534 ARG cc_start: 0.7782 (tpt-90) cc_final: 0.7445 (tpt-90)
REVERT: B  537 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7715 (pm20)
REVERT: A   58 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6270 (mm)
REVERT: A  318 MET cc_start: 0.5168 (ttt) cc_final: 0.4800 (mtm)
REVERT: A  427 ILE cc_start: 0.8858 (mp) cc_final: 0.8587 (mp)
REVERT: A  833 MET cc_start: 0.6718 (ptm) cc_final: 0.6336 (ptt)
REVERT: A  909 PHE cc_start: 0.7939 (t80) cc_final: 0.7651 (t80)
REVERT: A  979 ARG cc_start: 0.7939 (mtp180) cc_final: 0.7488 (tpt-90)
REVERT: A 1000 ASN cc_start: 0.7192 (t0) cc_final: 0.6501 (m-40)
REVERT: A 1039 PHE cc_start: 0.6647 (m-80) cc_final: 0.6320 (m-80)
  outliers start: 29
  outliers final: 17
  residues processed: 253
  average time/residue: 0.4191
  time to fit residues: 115.6258
Evaluate side-chains
  243 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 223
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  322 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  430 LYS
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain B residue  540 ASP
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  891 ASP
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  993 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 44 optimal weight:    0.0970
   chunk 13 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   chunk 18 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9980
   chunk 27 optimal weight:    8.9990
   chunk 100 optimal weight:    0.0670
   chunk 96 optimal weight:    0.7980
   chunk 108 optimal weight:    0.4980
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 202 ASN
** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 940 HIS ** 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 = 0.4731 r_free = 0.4731 target = 0.217935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.180001 restraints weight = 42218.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.4346 rms_B_bonded: 5.07
r_work (final): 0.4346
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4348 r_free = 0.4348    target_work(ls_wunit_k1) = 0.179         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4348 r_free = 0.4348    target_work(ls_wunit_k1) = 0.179         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6713
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  10859  Z= 0.139
  Angle     :  0.736  10.377  14651  Z= 0.364
  Chirality :  0.044   0.180   1581
  Planarity :  0.005   0.064   1883
  Dihedral  :  5.576  57.492   1437
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 25.40 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.82 (0.24), residues: 1281
  helix:  0.57 (0.21), residues: 608
  sheet: -1.90 (0.41), residues: 140
  loop : -1.42 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 472 
 TYR   0.015   0.001   TYR B 556 
 PHE   0.043   0.002   PHE A 667 
 TRP   0.017   0.001   TRP B 333 
 HIS   0.010   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (10859)
  covalent geometry    : angle       0.73630 (14651)
  hydrogen bonds       : bond        0.03498 (  495)
  hydrogen bonds       : angle       4.55989 ( 1437)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 234
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  367 ASP cc_start: 0.6357 (m-30) cc_final: 0.6127 (m-30)
REVERT: B  422 VAL cc_start: 0.6272 (OUTLIER) cc_final: 0.5882 (t)
REVERT: B  479 MET cc_start: 0.6977 (pp-130) cc_final: 0.6567 (pp-130)
REVERT: B  534 ARG cc_start: 0.7833 (tpt-90) cc_final: 0.7454 (tpt-90)
REVERT: B  537 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7616 (pm20)
REVERT: A   58 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6294 (mm)
REVERT: A  164 MET cc_start: 0.8056 (mpp) cc_final: 0.7773 (mpp)
REVERT: A  296 GLN cc_start: 0.7602 (tp40) cc_final: 0.7350 (tp40)
REVERT: A  427 ILE cc_start: 0.8514 (mp) cc_final: 0.8117 (mt)
REVERT: A  760 GLN cc_start: 0.7426 (pt0) cc_final: 0.7098 (pt0)
REVERT: A  833 MET cc_start: 0.6150 (ptm) cc_final: 0.5861 (ptt)
REVERT: A 1000 ASN cc_start: 0.6520 (t0) cc_final: 0.6025 (m-40)
  outliers start: 29
  outliers final: 15
  residues processed: 252
  average time/residue: 0.4094
  time to fit residues: 113.3393
Evaluate side-chains
  233 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 215
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  322 MET
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  430 LYS
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  891 ASP
Chi-restraints excluded: chain A residue  957 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 59 optimal weight:    0.3980
   chunk 41 optimal weight:    2.9990
   chunk 118 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 52 optimal weight:    0.0970
   chunk 110 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  59 HIS
** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 993 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.216189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.177732 restraints weight = 40163.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.4324 rms_B_bonded: 4.97
r_work: 0.4117 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4129
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4129 r_free = 0.4129    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4129 r_free = 0.4129    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4129
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  10859  Z= 0.152
  Angle     :  0.764  11.436  14651  Z= 0.376
  Chirality :  0.046   0.257   1581
  Planarity :  0.005   0.063   1883
  Dihedral  :  5.470  53.548   1437
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 25.83 %
    Favored  : 71.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.24), residues: 1281
  helix:  0.66 (0.21), residues: 597
  sheet: -1.92 (0.41), residues: 142
  loop : -1.29 (0.28), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1023 
 TYR   0.043   0.002   TYR A 432 
 PHE   0.040   0.002   PHE A 667 
 TRP   0.018   0.001   TRP A 780 
 HIS   0.013   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (10859)
  covalent geometry    : angle       0.76395 (14651)
  hydrogen bonds       : bond        0.03530 (  495)
  hydrogen bonds       : angle       4.53370 ( 1437)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 226
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  422 VAL cc_start: 0.6204 (OUTLIER) cc_final: 0.5839 (t)
REVERT: B  479 MET cc_start: 0.7408 (pp-130) cc_final: 0.6984 (pp-130)
REVERT: B  534 ARG cc_start: 0.7718 (tpt-90) cc_final: 0.7324 (tpt-90)
REVERT: B  537 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7700 (pm20)
REVERT: A   58 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6367 (mm)
REVERT: A  164 MET cc_start: 0.8230 (mpp) cc_final: 0.8001 (mpp)
REVERT: A  296 GLN cc_start: 0.7570 (tp40) cc_final: 0.7365 (tp40)
REVERT: A  427 ILE cc_start: 0.8727 (mp) cc_final: 0.8288 (mt)
REVERT: A  441 MET cc_start: 0.7342 (ppp) cc_final: 0.6778 (ppp)
REVERT: A  760 GLN cc_start: 0.7869 (pt0) cc_final: 0.7542 (pt0)
REVERT: A  833 MET cc_start: 0.6600 (ptm) cc_final: 0.6160 (ptt)
REVERT: A  875 HIS cc_start: 0.7546 (m-70) cc_final: 0.6552 (p-80)
REVERT: A  909 PHE cc_start: 0.7922 (t80) cc_final: 0.7666 (t80)
REVERT: A  979 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7205 (tpt-90)
REVERT: A 1000 ASN cc_start: 0.6947 (t0) cc_final: 0.6323 (m-40)
REVERT: A 1039 PHE cc_start: 0.6452 (m-80) cc_final: 0.6208 (m-80)
  outliers start: 29
  outliers final: 21
  residues processed: 241
  average time/residue: 0.3956
  time to fit residues: 105.0430
Evaluate side-chains
  241 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 217
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  322 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  430 LYS
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  993 GLN
Chi-restraints excluded: chain A residue 1042 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 98 optimal weight:    0.3980
   chunk 5 optimal weight:    5.9990
   chunk 119 optimal weight:    7.9990
   chunk 90 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 126 optimal weight:    0.5980
   chunk 115 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 320 ASN
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 586 GLN
A  59 HIS
A 202 ASN
** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 827 GLN
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 993 GLN
A1042 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4722 r_free = 0.4722 target = 0.216773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.177140 restraints weight = 51142.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.4309 rms_B_bonded: 6.28
r_work: 0.4077 rms_B_bonded: 5.89 restraints_weight: 2.0000
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4089
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4089 r_free = 0.4089    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4089 r_free = 0.4089    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4089
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.2978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10859  Z= 0.147
  Angle     :  0.769  12.975  14651  Z= 0.380
  Chirality :  0.045   0.252   1581
  Planarity :  0.005   0.062   1883
  Dihedral  :  5.357  48.943   1437
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 25.74 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.69 (0.24), residues: 1281
  helix:  0.68 (0.21), residues: 598
  sheet: -1.89 (0.41), residues: 142
  loop : -1.29 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1023 
 TYR   0.037   0.002   TYR A 432 
 PHE   0.040   0.002   PHE A 667 
 TRP   0.019   0.001   TRP A 780 
 HIS   0.017   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (10859)
  covalent geometry    : angle       0.76919 (14651)
  hydrogen bonds       : bond        0.03511 (  495)
  hydrogen bonds       : angle       4.51670 ( 1437)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 218
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 GLU cc_start: 0.7560 (pp20) cc_final: 0.7210 (pm20)
REVERT: B  422 VAL cc_start: 0.6227 (OUTLIER) cc_final: 0.5829 (t)
REVERT: B  479 MET cc_start: 0.7478 (pp-130) cc_final: 0.7046 (pp-130)
REVERT: B  534 ARG cc_start: 0.7732 (tpt-90) cc_final: 0.7331 (tpt-90)
REVERT: B  537 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7734 (pm20)
REVERT: B  563 MET cc_start: 0.6285 (ppp) cc_final: 0.4440 (mtm)
REVERT: A   58 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6303 (mm)
REVERT: A  164 MET cc_start: 0.8238 (mpp) cc_final: 0.8025 (mpp)
REVERT: A  427 ILE cc_start: 0.8697 (mp) cc_final: 0.8271 (mt)
REVERT: A  620 GLU cc_start: 0.7226 (pp20) cc_final: 0.6811 (tt0)
REVERT: A  833 MET cc_start: 0.6706 (ptm) cc_final: 0.6317 (ptt)
REVERT: A  939 ASP cc_start: 0.5383 (p0) cc_final: 0.5036 (t0)
REVERT: A  979 ARG cc_start: 0.7781 (mtp85) cc_final: 0.7204 (tpt-90)
REVERT: A 1000 ASN cc_start: 0.7020 (t0) cc_final: 0.6429 (m-40)
  outliers start: 36
  outliers final: 25
  residues processed: 240
  average time/residue: 0.4522
  time to fit residues: 119.0982
Evaluate side-chains
  242 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 214
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  322 MET
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  430 LYS
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain B residue  540 ASP
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   59 HIS
Chi-restraints excluded: chain A residue   63 GLN
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue  202 ASN
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  840 SER
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  993 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 44 optimal weight:    0.2980
   chunk 26 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0270
   chunk 40 optimal weight:    0.8980
   chunk 121 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 586 GLN
A  59 HIS
A 202 ASN
** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 993 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1042 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.216526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.177765 restraints weight = 46868.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.4317 rms_B_bonded: 5.84
r_work: 0.4094 rms_B_bonded: 5.59 restraints_weight: 2.0000
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4111 r_free = 0.4111    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4111 r_free = 0.4111    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.3025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.133  10859  Z= 0.291
  Angle     :  1.083  59.200  14651  Z= 0.609
  Chirality :  0.057   0.791   1581
  Planarity :  0.007   0.166   1883
  Dihedral  :  5.373  48.829   1437
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.70 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 26.76 %
    Favored  : 70.19 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.69 (0.24), residues: 1281
  helix:  0.69 (0.21), residues: 598
  sheet: -1.90 (0.41), residues: 142
  loop : -1.31 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1023 
 TYR   0.032   0.002   TYR A 432 
 PHE   0.039   0.002   PHE A 667 
 TRP   0.017   0.001   TRP A 780 
 HIS   0.232   0.005   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 (10859)
  covalent geometry    : angle       1.08331 (14651)
  hydrogen bonds       : bond        0.03528 (  495)
  hydrogen bonds       : angle       4.53752 ( 1437)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 216
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 GLU cc_start: 0.7520 (pp20) cc_final: 0.7176 (pm20)
REVERT: B  422 VAL cc_start: 0.6192 (OUTLIER) cc_final: 0.5817 (t)
REVERT: B  479 MET cc_start: 0.7430 (pp-130) cc_final: 0.6993 (pp-130)
REVERT: B  534 ARG cc_start: 0.7713 (tpt-90) cc_final: 0.7310 (tpt-90)
REVERT: B  537 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7720 (pm20)
REVERT: A  164 MET cc_start: 0.8237 (mpp) cc_final: 0.8009 (mpp)
REVERT: A  427 ILE cc_start: 0.8681 (mp) cc_final: 0.8258 (mt)
REVERT: A  833 MET cc_start: 0.6701 (ptm) cc_final: 0.6314 (ptt)
REVERT: A  875 HIS cc_start: 0.7600 (m-70) cc_final: 0.6592 (p-80)
REVERT: A  939 ASP cc_start: 0.5409 (p0) cc_final: 0.5068 (t0)
REVERT: A  979 ARG cc_start: 0.7757 (mtp85) cc_final: 0.7201 (tpt-90)
REVERT: A 1000 ASN cc_start: 0.6985 (t0) cc_final: 0.6397 (m-40)
REVERT: A 1033 GLN cc_start: 0.8459 (tp40) cc_final: 0.8236 (mp10)
  outliers start: 30
  outliers final: 21
  residues processed: 232
  average time/residue: 0.4628
  time to fit residues: 118.0177
Evaluate side-chains
  235 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 212
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  322 MET
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  430 LYS
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain B residue  540 ASP
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   63 GLN
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  840 SER
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  966 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 120 optimal weight:    0.8980
   chunk 73 optimal weight:    9.9990
   chunk 25 optimal weight:    0.8980
   chunk 54 optimal weight:    0.1980
   chunk 66 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 586 GLN
** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 993 GLN ** 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 = 0.4718 r_free = 0.4718 target = 0.216804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.178683 restraints weight = 43207.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.4324 rms_B_bonded: 5.45
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4322
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4322 r_free = 0.4322    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4322 r_free = 0.4322    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4322
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6737
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.133  10859  Z= 0.291
  Angle     :  1.083  59.200  14651  Z= 0.609
  Chirality :  0.057   0.791   1581
  Planarity :  0.007   0.166   1883
  Dihedral  :  5.373  48.829   1437
  Min Nonbonded Distance : 1.425

Molprobity Statistics.
  All-atom Clashscore : 19.08
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.70 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 27.27 %
    Favored  : 70.19 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.69 (0.24), residues: 1281
  helix:  0.69 (0.21), residues: 598
  sheet: -1.90 (0.41), residues: 142
  loop : -1.31 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1023 
 TYR   0.032   0.002   TYR A 432 
 PHE   0.039   0.002   PHE A 667 
 TRP   0.017   0.001   TRP A 780 
 HIS   0.232   0.005   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 (10859)
  covalent geometry    : angle       1.08331 (14651)
  hydrogen bonds       : bond        0.03528 (  495)
  hydrogen bonds       : angle       4.53752 ( 1437)

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 212
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 GLU cc_start: 0.7482 (pp20) cc_final: 0.7211 (pm20)
REVERT: B  422 VAL cc_start: 0.6255 (OUTLIER) cc_final: 0.5865 (t)
REVERT: B  479 MET cc_start: 0.7001 (pp-130) cc_final: 0.6570 (pp-130)
REVERT: B  534 ARG cc_start: 0.7809 (tpt-90) cc_final: 0.7396 (tpt-90)
REVERT: B  537 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7648 (pm20)
REVERT: A  164 MET cc_start: 0.8059 (mpp) cc_final: 0.7808 (mpp)
REVERT: A  427 ILE cc_start: 0.8479 (mp) cc_final: 0.8098 (mt)
REVERT: A  833 MET cc_start: 0.6278 (ptm) cc_final: 0.5992 (ptt)
REVERT: A  875 HIS cc_start: 0.7532 (m-70) cc_final: 0.6639 (p-80)
REVERT: A  939 ASP cc_start: 0.5116 (p0) cc_final: 0.4855 (t0)
REVERT: A  979 ARG cc_start: 0.7630 (mtp85) cc_final: 0.7173 (tpt-90)
REVERT: A 1000 ASN cc_start: 0.6529 (t0) cc_final: 0.5982 (m-40)
  outliers start: 24
  outliers final: 21
  residues processed: 226
  average time/residue: 0.4613
  time to fit residues: 115.1727
Evaluate side-chains
  234 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 211
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  322 MET
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  430 LYS
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain B residue  540 ASP
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   63 GLN
Chi-restraints excluded: chain A residue   90 CYS
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  712 LEU
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  748 LEU
Chi-restraints excluded: chain A residue  840 SER
Chi-restraints excluded: chain A residue  859 GLN
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  966 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 104 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9980
   chunk 102 optimal weight:    0.0980
   chunk 24 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 586 GLN
** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 993 GLN ** 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 = 0.4722 r_free = 0.4722 target = 0.216802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.177937 restraints weight = 47150.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.4316 rms_B_bonded: 5.84
r_work: 0.4092 rms_B_bonded: 5.63 restraints_weight: 2.0000
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4105 r_free = 0.4105    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4105 r_free = 0.4105    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.133  10859  Z= 0.291
  Angle     :  1.083  59.200  14651  Z= 0.609
  Chirality :  0.057   0.791   1581
  Planarity :  0.007   0.166   1883
  Dihedral  :  5.373  48.829   1437
  Min Nonbonded Distance : 1.425

Molprobity Statistics.
  All-atom Clashscore : 19.27
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.70 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 27.27 %
    Favored  : 70.19 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.69 (0.24), residues: 1281
  helix:  0.69 (0.21), residues: 598
  sheet: -1.90 (0.41), residues: 142
  loop : -1.31 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1023 
 TYR   0.032   0.002   TYR A 432 
 PHE   0.039   0.002   PHE A 667 
 TRP   0.017   0.001   TRP A 780 
 HIS   0.232   0.005   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 (10859)
  covalent geometry    : angle       1.08331 (14651)
  hydrogen bonds       : bond        0.03528 (  495)
  hydrogen bonds       : angle       4.53752 ( 1437)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3989.09 seconds
wall clock time: 68 minutes 48.49 seconds (4128.49 seconds total)