Starting phenix.real_space_refine
on Sun Apr  5 05:02:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ln6_63227/04_2026/9ln6_63227.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ln6_63227/04_2026/9ln6_63227.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ln6_63227/04_2026/9ln6_63227.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ln6_63227/04_2026/9ln6_63227.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ln6_63227/04_2026/9ln6_63227.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ln6_63227/04_2026/9ln6_63227.cif"
  }
  resolution = 3.49
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      76      5.16       5
     C    5156      2.51       5
     N    1394      2.21       5
     O    1504      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8130
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 937, 7491
          Classifications: {'peptide': 937}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 25, 'TRANS': 911}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 639
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 1, 'TRANS': 73}
  Time building chain proxies: 1.85, per 1000 atoms: 0.23
  Number of scatterers: 8130
  At special positions: 0
  Unit cell: (75.9, 97.9, 121, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      76     16.00
     O    1504      8.00
     N    1394      7.00
     C    5156      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: 0.66
  Conformation dependent library (CDL) restraints added in 247.2 milliseconds
  

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 5 sheets defined
      54.1% alpha, 9.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 137
    Processing helix  chain 'A' and resid 157 through 164
    Processing helix  chain 'A' and resid 188 through 203
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.805A  pdb=" N   ASN A 222 " --> pdb=" O   GLY A 218 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 218 through 222'
    Processing helix  chain 'A' and resid 229 through 234
      removed outlier: 3.857A  pdb=" N   ILE A 233 " --> pdb=" O   PHE A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 242
      removed outlier: 3.737A  pdb=" N   GLU A 241 " --> pdb=" O   PRO A 238 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   GLY A 242 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 238 through 242'
    Processing helix  chain 'A' and resid 243 through 252
      removed outlier: 3.729A  pdb=" N   ILE A 247 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   TYR A 249 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
      Proline residue:  A 251  - end of helix
    Processing helix  chain 'A' and resid 260 through 264
    Processing helix  chain 'A' and resid 271 through 275
    Processing helix  chain 'A' and resid 285 through 294
    Processing helix  chain 'A' and resid 311 through 319
      removed outlier: 3.565A  pdb=" N   GLN A 317 " --> pdb=" O   LYS A 313 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   LEU A 318 " --> pdb=" O   ARG A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 343
      removed outlier: 3.685A  pdb=" N   PHE A 343 " --> pdb=" O   ILE A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 359
      removed outlier: 3.963A  pdb=" N   ASN A 359 " --> pdb=" O   SER A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 368 through 386
    Processing helix  chain 'A' and resid 388 through 394
    Processing helix  chain 'A' and resid 395 through 407
      removed outlier: 3.692A  pdb=" N   LEU A 399 " --> pdb=" O   THR A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 438
    Processing helix  chain 'A' and resid 444 through 450
    Processing helix  chain 'A' and resid 453 through 463
    Processing helix  chain 'A' and resid 480 through 494
      removed outlier: 3.634A  pdb=" N   GLN A 484 " --> pdb=" O   HIS A 480 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   TYR A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   MET A 493 " --> pdb=" O   ALA A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 517
    Processing helix  chain 'A' and resid 522 through 524
      No H-bonds generated for 'chain 'A' and resid 522 through 524'
    Processing helix  chain 'A' and resid 525 through 535
    Processing helix  chain 'A' and resid 537 through 549
    Processing helix  chain 'A' and resid 555 through 569
      removed outlier: 3.679A  pdb=" N   LYS A 559 " --> pdb=" O   LYS A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 590
      removed outlier: 4.001A  pdb=" N   LEU A 580 " --> pdb=" O   GLN A 576 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLU A 588 " --> pdb=" O   HIS A 584 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   THR A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLN A 590 " --> pdb=" O   LEU A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 599
    Processing helix  chain 'A' and resid 611 through 623
    Processing helix  chain 'A' and resid 655 through 667
    Processing helix  chain 'A' and resid 667 through 672
      removed outlier: 3.545A  pdb=" N   THR A 671 " --> pdb=" O   SER A 667 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ASN A 672 " --> pdb=" O   VAL A 668 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 667 through 672'
    Processing helix  chain 'A' and resid 686 through 698
    Processing helix  chain 'A' and resid 718 through 728
      removed outlier: 3.652A  pdb=" N   ILE A 726 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   HIS A 727 " --> pdb=" O   THR A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 754
    Processing helix  chain 'A' and resid 774 through 785
    Processing helix  chain 'A' and resid 798 through 812
      removed outlier: 3.608A  pdb=" N   LEU A 805 " --> pdb=" O   ASP A 801 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   HIS A 812 " --> pdb=" O   GLU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 840
      removed outlier: 3.630A  pdb=" N   CYS A 832 " --> pdb=" O   THR A 828 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLU A 833 " --> pdb=" O   GLU A 829 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   TYR A 834 " --> pdb=" O   ALA A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 868
      removed outlier: 3.652A  pdb=" N   GLY A 859 " --> pdb=" O   LEU A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 885 through 897
      removed outlier: 3.818A  pdb=" N   SER A 889 " --> pdb=" O   THR A 885 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLU A 890 " --> pdb=" O   SER A 886 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   TYR A 891 " --> pdb=" O   LEU A 887 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU A 897 " --> pdb=" O   SER A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 912 through 925
      removed outlier: 3.601A  pdb=" N   GLY A 916 " --> pdb=" O   LEU A 912 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL A 923 " --> pdb=" O   LEU A 919 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 945 through 956
    Processing helix  chain 'A' and resid 969 through 982
    Processing helix  chain 'A' and resid 999 through 1001
      No H-bonds generated for 'chain 'A' and resid 999 through 1001'
    Processing helix  chain 'A' and resid 1002 through 1013
    Processing helix  chain 'A' and resid 1026 through 1039
      removed outlier: 3.574A  pdb=" N   LYS A1036 " --> pdb=" O   VAL A1032 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   VAL A1037 " --> pdb=" O   LYS A1033 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1051 through 1055
    Processing helix  chain 'A' and resid 1056 through 1070
    Processing helix  chain 'B' and resid 24 through 37
    Processing helix  chain 'B' and resid 39 through 41
      No H-bonds generated for 'chain 'B' and resid 39 through 41'
    Processing helix  chain 'B' and resid 57 through 62
    Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 217
      removed outlier: 6.343A  pdb=" N   TYR A 212 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   ILE A 257 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   PHE A 214 " --> pdb=" O   ILE A 257 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   ASP A 259 " --> pdb=" O   PHE A 214 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   LEU A 216 " --> pdb=" O   ASP A 259 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   LEU A 254 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   LEU A 304 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   PHE A 256 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   THR A 306 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   ILE A 258 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL A 179 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 228
    Processing sheet with id=AA3, first strand: chain 'A' and resid 442 through 443
    Processing sheet with id=AA4, first strand: chain 'A' and resid 604 through 609
      removed outlier: 3.624A  pdb=" N   VAL A 605 " --> pdb=" O   THR A 630 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ILE A 631 " --> pdb=" O   ASP A 679 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   TYR A 681 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU A 633 " --> pdb=" O   TYR A 681 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   LEU A 678 " --> pdb=" O   LEU A 708 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   LYS A 710 " --> pdb=" O   LEU A 678 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   LEU A 680 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   LEU A 848 " --> pdb=" O   VAL A 878 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LEU A 877 " --> pdb=" O   ASP A 906 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   LEU A 905 " --> pdb=" O   GLU A 935 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   LEU A 934 " --> pdb=" O   ASP A 963 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   LEU A 962 " --> pdb=" O   GLY A 992 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   MET A1019 " --> pdb=" O   GLY A1049 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 16
      removed outlier: 6.419A  pdb=" N   GLN B   4 " --> pdb=" O   ILE B  69 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   LEU B  71 " --> pdb=" O   GLN B   4 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   ARG B   6 " --> pdb=" O   LEU B  71 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   VAL B  73 " --> pdb=" O   ARG B   6 " (cutoff:3.500A)

    359 hydrogen bonds defined for protein.
    1029 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: 1.20

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2655
        1.34 -     1.46: 1441
        1.46 -     1.58: 4086
        1.58 -     1.70: 0
        1.70 -     1.81: 101
  Bond restraints: 8283
  Sorted by residual:
  bond pdb=" N   GLY A 123 "
       pdb=" CA  GLY A 123 "
    ideal  model  delta    sigma   weight residual
    1.451  1.492 -0.041 1.60e-02 3.91e+03 6.50e+00
  bond pdb=" CA  GLY A 992 "
       pdb=" C   GLY A 992 "
    ideal  model  delta    sigma   weight residual
    1.514  1.542 -0.028 1.41e-02 5.03e+03 3.97e+00
  bond pdb=" C   LEU A 991 "
       pdb=" N   GLY A 992 "
    ideal  model  delta    sigma   weight residual
    1.331  1.356 -0.026 1.46e-02 4.69e+03 3.14e+00
  bond pdb=" CB  CYS A 475 "
       pdb=" SG  CYS A 475 "
    ideal  model  delta    sigma   weight residual
    1.808  1.750  0.058 3.30e-02 9.18e+02 3.08e+00
  bond pdb=" CA  TYR A 476 "
       pdb=" CB  TYR A 476 "
    ideal  model  delta    sigma   weight residual
    1.536  1.494  0.042 2.53e-02 1.56e+03 2.71e+00
  ... (remaining 8278 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 10698
        1.41 -     2.81: 423
        2.81 -     4.22: 52
        4.22 -     5.62: 7
        5.62 -     7.03: 1
  Bond angle restraints: 11181
  Sorted by residual:
  angle pdb=" N   HIS A 323 "
        pdb=" CA  HIS A 323 "
        pdb=" CB  HIS A 323 "
      ideal   model   delta    sigma   weight residual
     110.90  105.28    5.62 1.56e+00 4.11e-01 1.30e+01
  angle pdb=" N   LYS A 225 "
        pdb=" CA  LYS A 225 "
        pdb=" C   LYS A 225 "
      ideal   model   delta    sigma   weight residual
     110.80  117.83   -7.03 2.13e+00 2.20e-01 1.09e+01
  angle pdb=" C   ASN A 321 "
        pdb=" CA  ASN A 321 "
        pdb=" CB  ASN A 321 "
      ideal   model   delta    sigma   weight residual
     112.27  106.99    5.28 1.75e+00 3.27e-01 9.10e+00
  angle pdb=" N   SER A 302 "
        pdb=" CA  SER A 302 "
        pdb=" C   SER A 302 "
      ideal   model   delta    sigma   weight residual
     109.95  113.99   -4.04 1.59e+00 3.96e-01 6.46e+00
  angle pdb=" N   VAL A 854 "
        pdb=" CA  VAL A 854 "
        pdb=" C   VAL A 854 "
      ideal   model   delta    sigma   weight residual
     106.21  108.85   -2.64 1.07e+00 8.73e-01 6.08e+00
  ... (remaining 11176 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.63: 4745
       16.63 -    33.26: 242
       33.26 -    49.89: 32
       49.89 -    66.51: 6
       66.51 -    83.14: 5
  Dihedral angle restraints: 5030
    sinusoidal: 2061
      harmonic: 2969
  Sorted by residual:
  dihedral pdb=" CA  TRP A1090 "
           pdb=" C   TRP A1090 "
           pdb=" N   TRP A1091 "
           pdb=" CA  TRP A1091 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.00  -26.00     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" CA  ASN A 420 "
           pdb=" C   ASN A 420 "
           pdb=" N   GLN A 421 "
           pdb=" CA  GLN A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.91  -16.09     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  GLN B   4 "
           pdb=" CB  GLN B   4 "
           pdb=" CG  GLN B   4 "
           pdb=" CD  GLN B   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.49  -59.51     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5027 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 773
       0.030 -    0.061: 341
       0.061 -    0.091: 117
       0.091 -    0.122: 31
       0.122 -    0.152: 10
  Chirality restraints: 1272
  Sorted by residual:
  chirality pdb=" CA  HIS A 323 "
            pdb=" N   HIS A 323 "
            pdb=" C   HIS A 323 "
            pdb=" CB  HIS A 323 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.77e-01
  chirality pdb=" CA  ILE A 178 "
            pdb=" N   ILE A 178 "
            pdb=" C   ILE A 178 "
            pdb=" CB  ILE A 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.27e-01
  chirality pdb=" CA  ILE A 257 "
            pdb=" N   ILE A 257 "
            pdb=" C   ILE A 257 "
            pdb=" CB  ILE A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 1269 not shown)

  Planarity restraints: 1417
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 602 "   -0.038 5.00e-02 4.00e+02   5.80e-02 5.39e+00
        pdb=" N   PRO A 603 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 603 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 603 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 443 "   -0.022 2.00e-02 2.50e+03   1.23e-02 3.01e+00
        pdb=" CG  TYR A 443 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 443 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 443 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 443 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 443 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 443 "   -0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 443 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 573 "    0.026 5.00e-02 4.00e+02   3.88e-02 2.41e+00
        pdb=" N   PRO A 574 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 574 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 574 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1414 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 58
        2.59 -     3.17: 6934
        3.17 -     3.75: 11460
        3.75 -     4.32: 16517
        4.32 -     4.90: 27374
  Nonbonded interactions: 62343
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 230 "
            pdb=" OG  SER A 234 "
     model   vdw
     2.014 3.040
  nonbonded pdb=" N   GLU A 245 "
            pdb=" OE1 GLU A 245 "
     model   vdw
     2.067 3.120
  nonbonded pdb=" OD2 ASP A 914 "
            pdb=" OG1 THR A 942 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OE1 GLU A 220 "
            pdb=" OH  TYR A 472 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   ARG A 219 "
            pdb=" OH  TYR A 443 "
     model   vdw
     2.246 3.040
  ... (remaining 62338 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     8.600
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6465
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      :  0.006   0.058   8283  Z= 0.256
  Angle     :  0.647   7.029  11181  Z= 0.373
  Chirality :  0.040   0.152   1272
  Planarity :  0.004   0.058   1417
  Dihedral  : 10.628  83.142   3096
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  3.12 %
    Favored  : 96.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.27), residues: 1002
  helix:  0.81 (0.24), residues: 456
  sheet: -1.40 (0.47), residues: 120
  loop :  0.22 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 227 
 TYR   0.023   0.002   TYR A 443 
 PHE   0.020   0.002   PHE A 287 
 TRP   0.009   0.002   TRP A 498 
 HIS   0.007   0.001   HIS A 524 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 ( 8283)
  covalent geometry    : angle       0.64687 (11181)
  hydrogen bonds       : bond        0.20132 (  359)
  hydrogen bonds       : angle       7.03449 ( 1029)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 266
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  485 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7982 (mt-10)
REVERT: A  492 TYR cc_start: 0.7624 (m-80) cc_final: 0.7209 (m-80)
  outliers start: 5
  outliers final: 2
  residues processed: 271
  average time/residue: 0.0953
  time to fit residues: 33.7625
Evaluate side-chains
  132 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  688 SER
Chi-restraints excluded: chain A residue 1093 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 317 GLN
A 446 ASN
A 694 HIS
A 701 ASN
A 733 HIS
A 786 GLN
** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 883 HIS
A 966 ASN
** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.127635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.094084 restraints weight = 21211.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 4.94
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.3948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8283  Z= 0.139
  Angle     :  0.658  10.264  11181  Z= 0.332
  Chirality :  0.042   0.201   1272
  Planarity :  0.004   0.042   1417
  Dihedral  :  4.583  57.952   1086
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 12.50 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.28), residues: 1002
  helix:  1.65 (0.24), residues: 466
  sheet: -0.58 (0.48), residues: 131
  loop :  0.59 (0.33), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 811 
 TYR   0.023   0.001   TYR A 983 
 PHE   0.014   0.001   PHE A 353 
 TRP   0.017   0.002   TRP A1089 
 HIS   0.008   0.001   HIS A 904 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8283)
  covalent geometry    : angle       0.65757 (11181)
  hydrogen bonds       : bond        0.04487 (  359)
  hydrogen bonds       : angle       5.09915 ( 1029)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7930 (tm-30)
REVERT: A  320 LYS cc_start: 0.7031 (mttt) cc_final: 0.6590 (ptpt)
REVERT: A  485 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8247 (mt-10)
REVERT: A  618 SER cc_start: 0.9074 (m) cc_final: 0.8515 (p)
REVERT: A  798 LEU cc_start: 0.8806 (mt) cc_final: 0.8430 (pp)
REVERT: A  810 LEU cc_start: 0.9199 (tt) cc_final: 0.8967 (tt)
REVERT: A  884 PHE cc_start: 0.7522 (m-10) cc_final: 0.6796 (m-10)
REVERT: A  937 MET cc_start: 0.9192 (ttp) cc_final: 0.8933 (tpp)
REVERT: B   68 THR cc_start: 0.8210 (m) cc_final: 0.7981 (p)
  outliers start: 25
  outliers final: 12
  residues processed: 158
  average time/residue: 0.0845
  time to fit residues: 18.3447
Evaluate side-chains
  128 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 GLU
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  550 CYS
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  733 HIS
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  807 CYS
Chi-restraints excluded: chain A residue  935 GLU
Chi-restraints excluded: chain A residue  953 ILE
Chi-restraints excluded: chain A residue 1093 PHE
Chi-restraints excluded: chain B residue   13 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 84 optimal weight:    9.9990
   chunk 58 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   chunk 33 optimal weight:    0.1980
   chunk 76 optimal weight:    4.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 446 ASN
A 516 GLN
** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  43 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.123487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.089932 restraints weight = 21007.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 4.86
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.4894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8283  Z= 0.164
  Angle     :  0.606   8.468  11181  Z= 0.311
  Chirality :  0.041   0.146   1272
  Planarity :  0.004   0.043   1417
  Dihedral  :  4.350  42.955   1085
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 13.58 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.28), residues: 1002
  helix:  1.72 (0.24), residues: 465
  sheet: -0.78 (0.45), residues: 139
  loop :  0.61 (0.34), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 811 
 TYR   0.016   0.002   TYR A 681 
 PHE   0.015   0.001   PHE A 486 
 TRP   0.014   0.002   TRP A1089 
 HIS   0.015   0.001   HIS A 733 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 8283)
  covalent geometry    : angle       0.60570 (11181)
  hydrogen bonds       : bond        0.04439 (  359)
  hydrogen bonds       : angle       4.91198 ( 1029)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 SER cc_start: 0.8583 (m) cc_final: 0.8122 (p)
REVERT: A  320 LYS cc_start: 0.7529 (mttt) cc_final: 0.7328 (ptpt)
REVERT: A  485 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8240 (mt-10)
REVERT: A  492 TYR cc_start: 0.8441 (m-80) cc_final: 0.7541 (m-80)
REVERT: A  621 CYS cc_start: 0.8413 (m) cc_final: 0.8132 (m)
REVERT: A  690 MET cc_start: 0.8821 (mmm) cc_final: 0.8546 (mmt)
REVERT: A  728 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8266 (t0)
REVERT: A  750 CYS cc_start: 0.8862 (p) cc_final: 0.8606 (p)
REVERT: A  788 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8048 (tt)
REVERT: A  868 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7227 (mm-40)
REVERT: A  884 PHE cc_start: 0.7404 (m-10) cc_final: 0.7147 (m-10)
REVERT: A  937 MET cc_start: 0.9231 (ttp) cc_final: 0.8930 (tpp)
REVERT: A 1004 GLN cc_start: 0.9069 (tp40) cc_final: 0.8663 (tm-30)
REVERT: B   43 GLN cc_start: 0.7200 (pt0) cc_final: 0.6907 (pt0)
REVERT: B   68 THR cc_start: 0.8222 (m) cc_final: 0.7911 (p)
  outliers start: 27
  outliers final: 17
  residues processed: 146
  average time/residue: 0.0961
  time to fit residues: 18.8183
Evaluate side-chains
  132 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  592 LYS
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  728 ASN
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  807 CYS
Chi-restraints excluded: chain A residue  828 THR
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  953 ILE
Chi-restraints excluded: chain A residue 1093 PHE
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   37 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 92 optimal weight:    0.2980
   chunk 36 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
A 446 ASN
A 728 ASN
** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.124775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.088266 restraints weight = 21138.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 4.81
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.5372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8283  Z= 0.106
  Angle     :  0.548   9.812  11181  Z= 0.276
  Chirality :  0.038   0.136   1272
  Planarity :  0.004   0.043   1417
  Dihedral  :  4.003  37.236   1085
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.36 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.28), residues: 1002
  helix:  1.94 (0.24), residues: 468
  sheet: -0.61 (0.47), residues: 128
  loop :  0.61 (0.34), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  29 
 TYR   0.012   0.001   TYR A 443 
 PHE   0.010   0.001   PHE A 486 
 TRP   0.008   0.001   TRP A1089 
 HIS   0.004   0.001   HIS A 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8283)
  covalent geometry    : angle       0.54758 (11181)
  hydrogen bonds       : bond        0.03370 (  359)
  hydrogen bonds       : angle       4.56645 ( 1029)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 SER cc_start: 0.8675 (m) cc_final: 0.7917 (p)
REVERT: A  263 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7162 (mp0)
REVERT: A  320 LYS cc_start: 0.7667 (mttt) cc_final: 0.7176 (ptpt)
REVERT: A  350 MET cc_start: 0.8864 (ppp) cc_final: 0.8291 (ppp)
REVERT: A  485 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8171 (mt-10)
REVERT: A  492 TYR cc_start: 0.8626 (m-80) cc_final: 0.8078 (m-80)
REVERT: A  621 CYS cc_start: 0.8105 (m) cc_final: 0.7739 (m)
REVERT: A  728 ASN cc_start: 0.8311 (t0) cc_final: 0.8078 (t0)
REVERT: A  750 CYS cc_start: 0.8769 (p) cc_final: 0.8500 (p)
REVERT: A  884 PHE cc_start: 0.7422 (m-10) cc_final: 0.7179 (m-10)
REVERT: A  937 MET cc_start: 0.9326 (ttp) cc_final: 0.9039 (tpp)
REVERT: A 1004 GLN cc_start: 0.9196 (tp40) cc_final: 0.8812 (tm-30)
REVERT: B   64 ARG cc_start: 0.7759 (tpp80) cc_final: 0.7217 (tpp80)
REVERT: B   68 THR cc_start: 0.8247 (m) cc_final: 0.7725 (p)
  outliers start: 25
  outliers final: 12
  residues processed: 145
  average time/residue: 0.0848
  time to fit residues: 16.8711
Evaluate side-chains
  131 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  816 TYR
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  953 ILE
Chi-restraints excluded: chain A residue 1093 PHE
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   37 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 10 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0970
   chunk 29 optimal weight:    0.4980
   chunk 8 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 506 GLN
A 786 GLN
** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.124676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.092829 restraints weight = 20995.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 5.04
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.5646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8283  Z= 0.100
  Angle     :  0.554   8.765  11181  Z= 0.275
  Chirality :  0.039   0.132   1272
  Planarity :  0.003   0.044   1417
  Dihedral  :  3.849  34.286   1085
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.87 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.28), residues: 1002
  helix:  2.03 (0.24), residues: 465
  sheet: -0.46 (0.46), residues: 132
  loop :  0.70 (0.34), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 347 
 TYR   0.015   0.001   TYR A 983 
 PHE   0.009   0.001   PHE A 400 
 TRP   0.007   0.001   TRP A1089 
 HIS   0.003   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 8283)
  covalent geometry    : angle       0.55419 (11181)
  hydrogen bonds       : bond        0.03181 (  359)
  hydrogen bonds       : angle       4.45473 ( 1029)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7194 (mp0)
REVERT: A  330 MET cc_start: 0.9002 (tpp) cc_final: 0.8765 (tpt)
REVERT: A  485 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8142 (mt-10)
REVERT: A  510 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8160 (m-30)
REVERT: A  552 MET cc_start: 0.8340 (mmp) cc_final: 0.8001 (mmm)
REVERT: A  690 MET cc_start: 0.8410 (mpp) cc_final: 0.8177 (mpp)
REVERT: A  728 ASN cc_start: 0.8396 (t0) cc_final: 0.8163 (t0)
REVERT: A  741 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8393 (mp)
REVERT: A  750 CYS cc_start: 0.8772 (p) cc_final: 0.8422 (p)
REVERT: A  798 LEU cc_start: 0.8806 (mt) cc_final: 0.8351 (pt)
REVERT: A  816 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7390 (m-80)
REVERT: A  884 PHE cc_start: 0.7361 (m-10) cc_final: 0.7057 (m-10)
REVERT: A  954 LEU cc_start: 0.8736 (tt) cc_final: 0.8494 (mt)
REVERT: A 1004 GLN cc_start: 0.9062 (tp40) cc_final: 0.8711 (tm-30)
REVERT: B   64 ARG cc_start: 0.7696 (tpp80) cc_final: 0.7335 (tpp80)
REVERT: B   68 THR cc_start: 0.8033 (m) cc_final: 0.7358 (p)
  outliers start: 23
  outliers final: 13
  residues processed: 137
  average time/residue: 0.0808
  time to fit residues: 15.3568
Evaluate side-chains
  126 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  510 ASP
Chi-restraints excluded: chain A residue  592 LYS
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  741 ILE
Chi-restraints excluded: chain A residue  782 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  816 TYR
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  953 ILE
Chi-restraints excluded: chain A residue 1093 PHE
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   37 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0980
   chunk 59 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0870
   chunk 45 optimal weight:    0.9990
   chunk 94 optimal weight:    9.9990
   chunk 89 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    0.5960

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

Flipped N/Q/H residues before XYZ refinement:
** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.124134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.092620 restraints weight = 21004.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 4.94
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.5949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8283  Z= 0.098
  Angle     :  0.549   9.332  11181  Z= 0.274
  Chirality :  0.038   0.139   1272
  Planarity :  0.003   0.043   1417
  Dihedral  :  3.746  31.434   1085
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.38 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.28), residues: 1002
  helix:  2.00 (0.24), residues: 466
  sheet: -0.55 (0.46), residues: 133
  loop :  0.65 (0.34), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 925 
 TYR   0.018   0.001   TYR A 212 
 PHE   0.008   0.001   PHE A 229 
 TRP   0.027   0.002   TRP B   2 
 HIS   0.003   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 8283)
  covalent geometry    : angle       0.54904 (11181)
  hydrogen bonds       : bond        0.03148 (  359)
  hydrogen bonds       : angle       4.44494 ( 1029)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7221 (mp0)
REVERT: A  330 MET cc_start: 0.8975 (tpp) cc_final: 0.8753 (tpt)
REVERT: A  485 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8108 (mt-10)
REVERT: A  552 MET cc_start: 0.8324 (mmp) cc_final: 0.8002 (mmm)
REVERT: A  618 SER cc_start: 0.8950 (m) cc_final: 0.8417 (p)
REVERT: A  690 MET cc_start: 0.8454 (mpp) cc_final: 0.8075 (mmt)
REVERT: A  750 CYS cc_start: 0.8774 (p) cc_final: 0.8419 (p)
REVERT: A  816 TYR cc_start: 0.7634 (t80) cc_final: 0.7303 (m-80)
REVERT: A  884 PHE cc_start: 0.7281 (m-10) cc_final: 0.6980 (m-10)
REVERT: A  937 MET cc_start: 0.8279 (tpp) cc_final: 0.7931 (tpp)
REVERT: A 1004 GLN cc_start: 0.9018 (tp40) cc_final: 0.8665 (tm-30)
REVERT: A 1019 MET cc_start: 0.8249 (tmm) cc_final: 0.7871 (tmm)
REVERT: B   52 MET cc_start: 0.8567 (mtm) cc_final: 0.8192 (mtt)
  outliers start: 23
  outliers final: 12
  residues processed: 143
  average time/residue: 0.0817
  time to fit residues: 16.1707
Evaluate side-chains
  128 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  953 ILE
Chi-restraints excluded: chain A residue 1090 TRP
Chi-restraints excluded: chain B residue   12 GLN
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   37 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 86 optimal weight:    8.9990
   chunk 94 optimal weight:    6.9990
   chunk 26 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 89 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0570
   overall best weight:    0.8500

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

Flipped N/Q/H residues before XYZ refinement:
** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.123482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.087678 restraints weight = 21682.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 4.82
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.6235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8283  Z= 0.111
  Angle     :  0.605  13.813  11181  Z= 0.291
  Chirality :  0.039   0.143   1272
  Planarity :  0.003   0.043   1417
  Dihedral  :  3.735  18.136   1083
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 17.56 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.28), residues: 1002
  helix:  1.85 (0.24), residues: 473
  sheet: -0.57 (0.46), residues: 129
  loop :  0.52 (0.34), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 925 
 TYR   0.017   0.001   TYR A 212 
 PHE   0.010   0.001   PHE A 486 
 TRP   0.020   0.002   TRP A1089 
 HIS   0.003   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8283)
  covalent geometry    : angle       0.60515 (11181)
  hydrogen bonds       : bond        0.03328 (  359)
  hydrogen bonds       : angle       4.55015 ( 1029)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 SER cc_start: 0.8621 (m) cc_final: 0.8185 (m)
REVERT: A  263 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7074 (mp0)
REVERT: A  485 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8104 (mt-10)
REVERT: A  552 MET cc_start: 0.8236 (mmp) cc_final: 0.7921 (mmm)
REVERT: A  690 MET cc_start: 0.8506 (mpp) cc_final: 0.8097 (mmt)
REVERT: A  728 ASN cc_start: 0.8449 (t0) cc_final: 0.8237 (t0)
REVERT: A  750 CYS cc_start: 0.8851 (p) cc_final: 0.8491 (p)
REVERT: A  884 PHE cc_start: 0.7420 (m-10) cc_final: 0.7054 (m-10)
REVERT: A 1004 GLN cc_start: 0.9202 (tp40) cc_final: 0.8812 (tm-30)
REVERT: A 1019 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8487 (tmm)
  outliers start: 19
  outliers final: 13
  residues processed: 133
  average time/residue: 0.0785
  time to fit residues: 14.5687
Evaluate side-chains
  125 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain A residue  592 LYS
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  721 ILE
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  953 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue 1019 MET
Chi-restraints excluded: chain A residue 1090 TRP
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   37 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.122498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.090415 restraints weight = 21358.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 5.03
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.6447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8283  Z= 0.115
  Angle     :  0.619  13.557  11181  Z= 0.297
  Chirality :  0.040   0.250   1272
  Planarity :  0.003   0.045   1417
  Dihedral  :  3.755  15.948   1083
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.35 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.28), residues: 1002
  helix:  1.84 (0.24), residues: 474
  sheet: -0.55 (0.46), residues: 129
  loop :  0.48 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 925 
 TYR   0.016   0.001   TYR A 212 
 PHE   0.009   0.001   PHE A 486 
 TRP   0.019   0.002   TRP A1089 
 HIS   0.003   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8283)
  covalent geometry    : angle       0.61882 (11181)
  hydrogen bonds       : bond        0.03355 (  359)
  hydrogen bonds       : angle       4.55440 ( 1029)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 TYR cc_start: 0.8604 (m-10) cc_final: 0.8224 (m-10)
REVERT: A  260 SER cc_start: 0.8676 (m) cc_final: 0.8303 (m)
REVERT: A  263 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7135 (mp0)
REVERT: A  485 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8104 (mt-10)
REVERT: A  552 MET cc_start: 0.8301 (mmp) cc_final: 0.8056 (mmm)
REVERT: A  690 MET cc_start: 0.8583 (mpp) cc_final: 0.8145 (mmt)
REVERT: A  750 CYS cc_start: 0.8808 (p) cc_final: 0.8453 (p)
REVERT: A  884 PHE cc_start: 0.7287 (m-10) cc_final: 0.6896 (m-10)
REVERT: A  926 HIS cc_start: 0.8543 (m90) cc_final: 0.8205 (p90)
REVERT: A 1004 GLN cc_start: 0.9074 (tp40) cc_final: 0.8682 (tm-30)
REVERT: B   20 SER cc_start: 0.7318 (t) cc_final: 0.7063 (p)
REVERT: B   30 ARG cc_start: 0.9178 (mmm-85) cc_final: 0.8915 (mmm-85)
REVERT: B   52 MET cc_start: 0.8613 (mtm) cc_final: 0.8260 (mtt)
REVERT: B   66 ASN cc_start: 0.8297 (m-40) cc_final: 0.7958 (m-40)
  outliers start: 24
  outliers final: 17
  residues processed: 136
  average time/residue: 0.0789
  time to fit residues: 15.0136
Evaluate side-chains
  128 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  816 TYR
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  953 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue 1090 TRP
Chi-restraints excluded: chain A residue 1093 PHE
Chi-restraints excluded: chain B residue   12 GLN
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   68 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 90 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 42 optimal weight:    0.4980
   chunk 91 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.123351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.087340 restraints weight = 21531.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 4.83
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.6654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8283  Z= 0.110
  Angle     :  0.622  12.818  11181  Z= 0.296
  Chirality :  0.040   0.336   1272
  Planarity :  0.003   0.045   1417
  Dihedral  :  3.733  16.385   1083
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.00 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.28), residues: 1002
  helix:  1.78 (0.24), residues: 474
  sheet: -0.47 (0.46), residues: 130
  loop :  0.47 (0.34), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 925 
 TYR   0.015   0.001   TYR A 212 
 PHE   0.009   0.001   PHE A 486 
 TRP   0.022   0.002   TRP A1089 
 HIS   0.004   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8283)
  covalent geometry    : angle       0.62239 (11181)
  hydrogen bonds       : bond        0.03246 (  359)
  hydrogen bonds       : angle       4.52689 ( 1029)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 TYR cc_start: 0.8607 (m-10) cc_final: 0.8292 (m-10)
REVERT: A  260 SER cc_start: 0.8610 (m) cc_final: 0.8157 (m)
REVERT: A  263 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7031 (mp0)
REVERT: A  330 MET cc_start: 0.9102 (tpt) cc_final: 0.8430 (tpp)
REVERT: A  485 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8091 (mt-10)
REVERT: A  552 MET cc_start: 0.8249 (mmp) cc_final: 0.7993 (mmm)
REVERT: A  690 MET cc_start: 0.8599 (mpp) cc_final: 0.8159 (mmt)
REVERT: A  750 CYS cc_start: 0.8805 (p) cc_final: 0.8455 (p)
REVERT: A  884 PHE cc_start: 0.7345 (m-10) cc_final: 0.6941 (m-10)
REVERT: A  926 HIS cc_start: 0.8554 (m90) cc_final: 0.8237 (p90)
REVERT: A 1004 GLN cc_start: 0.9188 (tp40) cc_final: 0.8805 (tm-30)
REVERT: A 1019 MET cc_start: 0.8418 (tmm) cc_final: 0.8073 (tmm)
REVERT: B   20 SER cc_start: 0.7444 (t) cc_final: 0.7229 (p)
REVERT: B   66 ASN cc_start: 0.8353 (m-40) cc_final: 0.8021 (m-40)
  outliers start: 20
  outliers final: 18
  residues processed: 128
  average time/residue: 0.0730
  time to fit residues: 13.2722
Evaluate side-chains
  124 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  953 ILE
Chi-restraints excluded: chain A residue  959 LEU
Chi-restraints excluded: chain A residue 1090 TRP
Chi-restraints excluded: chain A residue 1093 PHE
Chi-restraints excluded: chain B residue   12 GLN
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   68 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0980
   chunk 54 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.123141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.087098 restraints weight = 21485.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 4.80
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.6846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8283  Z= 0.111
  Angle     :  0.641  13.971  11181  Z= 0.303
  Chirality :  0.040   0.411   1272
  Planarity :  0.003   0.046   1417
  Dihedral  :  3.672  16.049   1083
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.43 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.28), residues: 1002
  helix:  1.77 (0.24), residues: 475
  sheet: -0.52 (0.46), residues: 133
  loop :  0.48 (0.34), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  30 
 TYR   0.014   0.001   TYR A 212 
 PHE   0.009   0.001   PHE A 486 
 TRP   0.023   0.002   TRP A1089 
 HIS   0.004   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8283)
  covalent geometry    : angle       0.64071 (11181)
  hydrogen bonds       : bond        0.03229 (  359)
  hydrogen bonds       : angle       4.50689 ( 1029)

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

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

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 TYR cc_start: 0.8552 (m-10) cc_final: 0.8327 (m-10)
REVERT: A  260 SER cc_start: 0.8610 (m) cc_final: 0.8168 (m)
REVERT: A  263 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7039 (mp0)
REVERT: A  330 MET cc_start: 0.9043 (tpt) cc_final: 0.8389 (tpp)
REVERT: A  485 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8054 (mt-10)
REVERT: A  552 MET cc_start: 0.8352 (mmp) cc_final: 0.8075 (mmm)
REVERT: A  690 MET cc_start: 0.8604 (mpp) cc_final: 0.8159 (mmt)
REVERT: A  750 CYS cc_start: 0.8847 (p) cc_final: 0.8529 (p)
REVERT: A  884 PHE cc_start: 0.7366 (m-10) cc_final: 0.7057 (m-10)
REVERT: A  926 HIS cc_start: 0.8545 (m90) cc_final: 0.8254 (p90)
REVERT: A 1004 GLN cc_start: 0.9131 (tp40) cc_final: 0.8763 (tm-30)
REVERT: B   66 ASN cc_start: 0.8263 (m-40) cc_final: 0.7990 (m-40)
  outliers start: 18
  outliers final: 17
  residues processed: 121
  average time/residue: 0.0784
  time to fit residues: 13.3082
Evaluate side-chains
  121 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  371 VAL
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  902 LEU
Chi-restraints excluded: chain A residue  953 ILE
Chi-restraints excluded: chain A residue 1090 TRP
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain B residue   12 GLN
Chi-restraints excluded: chain B residue   13 THR
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   68 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 59 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.121751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.088329 restraints weight = 21616.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 4.98
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.6977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8283  Z= 0.133
  Angle     :  0.657  14.165  11181  Z= 0.312
  Chirality :  0.041   0.393   1272
  Planarity :  0.004   0.047   1417
  Dihedral  :  3.814  16.033   1083
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.75 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.28), residues: 1002
  helix:  1.76 (0.25), residues: 474
  sheet: -0.42 (0.47), residues: 131
  loop :  0.37 (0.34), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 784 
 TYR   0.016   0.001   TYR A 212 
 PHE   0.010   0.001   PHE A 486 
 TRP   0.024   0.002   TRP A 348 
 HIS   0.004   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8283)
  covalent geometry    : angle       0.65667 (11181)
  hydrogen bonds       : bond        0.03569 (  359)
  hydrogen bonds       : angle       4.56804 ( 1029)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1589.70 seconds
wall clock time: 28 minutes 9.39 seconds (1689.39 seconds total)