Starting phenix.real_space_refine
on Fri Aug 22 17:27:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h3u_32828/08_2025/8h3u_32828.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h3u_32828/08_2025/8h3u_32828.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h3u_32828/08_2025/8h3u_32828.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h3u_32828/08_2025/8h3u_32828.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h3u_32828/08_2025/8h3u_32828.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h3u_32828/08_2025/8h3u_32828.map"
  }
  resolution = 4.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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      44      5.16       5
     C    4023      2.51       5
     N    1076      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6383
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4539
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 583, 4539
          Classifications: {'peptide': 583}
          Link IDs: {'PTRANS': 28, 'TRANS': 554}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1844
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 220}
  Time building chain proxies: 1.63, per 1000 atoms: 0.26
  Number of scatterers: 6383
  At special positions: 0
  Unit cell: (94.14, 94.14, 154.808, 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      44     16.00
     O    1240      8.00
     N    1076      7.00
     C    4023      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 184 " - pdb=" SG  CYS A 197 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 191 " - pdb=" SG  CYS A 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 204 " - pdb=" SG  CYS A 221 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 225 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 347 " - pdb=" SG  CYS A 354 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 422 " - pdb=" SG  CYS A 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 650 " - pdb=" SG  CYS A 668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 677 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 716 " - pdb=" SG  CYS A 767 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 772 " - pdb=" SG  CYS B 896 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 810 " - pdb=" SG  CYS B 826 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 910 " - pdb=" SG  CYS B 977 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 941 " - pdb=" SG  CYS B 956 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 967 " - pdb=" SG  CYS B 995 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 351.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1496

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 13 sheets defined
      8.1% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 201 through 203
      No H-bonds generated for 'chain 'A' and resid 201 through 203'
    Processing helix  chain 'A' and resid 213 through 217
    Processing helix  chain 'A' and resid 286 through 290
      removed outlier: 3.762A  pdb=" N   SER A 289 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A 290 " --> pdb=" O   GLY A 287 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 286 through 290'
    Processing helix  chain 'A' and resid 340 through 346
    Processing helix  chain 'A' and resid 531 through 534
    Processing helix  chain 'A' and resid 671 through 675
    Processing helix  chain 'A' and resid 708 through 719
    Processing helix  chain 'B' and resid 833 through 835
      No H-bonds generated for 'chain 'B' and resid 833 through 835'
    Processing helix  chain 'B' and resid 937 through 945
    Processing helix  chain 'B' and resid 1007 through 1009
      No H-bonds generated for 'chain 'B' and resid 1007 through 1009'
    Processing helix  chain 'B' and resid 1010 through 1019
      removed outlier: 3.965A  pdb=" N   PHE B1017 " --> pdb=" O   TRP B1013 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   HIS B1019 " --> pdb=" O   GLN B1015 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190
      removed outlier: 3.732A  pdb=" N   ILE A 198 " --> pdb=" O   SER A 189 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 231
      removed outlier: 6.433A  pdb=" N   LEU A 280 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   SER A 295 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   ILE A 282 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 239
      removed outlier: 3.537A  pdb=" N   GLY A 236 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   GLY A 326 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   PHE A 272 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   ASN A 328 " --> pdb=" O   ASP A 270 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358
    Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 370
      removed outlier: 3.704A  pdb=" N   ILE A 369 " --> pdb=" O   TYR A 393 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   TYR A 393 " --> pdb=" O   ILE A 369 " (cutoff:3.500A)
      removed outlier: 12.752A  pdb=" N   PHE A 392 " --> pdb=" O   ASP A 494 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ASP A 494 " --> pdb=" O   PHE A 392 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE A 394 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   LEU A 492 " --> pdb=" O   HIS A 428 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   HIS A 428 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   ASP A 494 " --> pdb=" O   TRP A 426 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   TRP A 426 " --> pdb=" O   ASP A 494 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 405 through 407
      removed outlier: 3.521A  pdb=" N   SER A 438 " --> pdb=" O   ASN A 480 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE A 482 " --> pdb=" O   LYS A 436 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   LYS A 436 " --> pdb=" O   PHE A 482 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   PHE A 452 " --> pdb=" O   ILE A 439 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   ILE A 441 " --> pdb=" O   THR A 450 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   THR A 450 " --> pdb=" O   ILE A 441 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537
      removed outlier: 3.696A  pdb=" N   PHE A 537 " --> pdb=" O   ALA A 629 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ALA A 629 " --> pdb=" O   PHE A 537 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ASN A 630 " --> pdb=" O   PHE A 568 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   PHE A 568 " --> pdb=" O   ASN A 630 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   THR A 632 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   LEU A 566 " --> pdb=" O   THR A 632 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 594 through 596
      removed outlier: 3.695A  pdb=" N   ALA A 594 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 693 through 694
    Processing sheet with id=AB1, first strand: chain 'A' and resid 724 through 729
      removed outlier: 3.631A  pdb=" N   GLN A 766 " --> pdb=" O   SER A 726 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS A 728 " --> pdb=" O   ARG A 764 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 740 through 743
      removed outlier: 3.570A  pdb=" N   THR A 752 " --> pdb=" O   LYS A 740 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 789 through 790
      removed outlier: 3.687A  pdb=" N   SER B 789 " --> pdb=" O   GLU B 930 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLN B 929 " --> pdb=" O   GLY B 914 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLY B 914 " --> pdb=" O   GLN B 929 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ALA B 913 " --> pdb=" O   PRO B 974 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY B 987 " --> pdb=" O   LEU B 975 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   CYS B 977 " --> pdb=" O   LEU B 985 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   LEU B 985 " --> pdb=" O   CYS B 977 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   VAL B1003 " --> pdb=" O   SER B 990 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 808 through 812
      removed outlier: 6.242A  pdb=" N   LEU B 808 " --> pdb=" O   TYR B 804 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   TYR B 804 " --> pdb=" O   LEU B 808 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   CYS B 810 " --> pdb=" O   LEU B 802 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LEU B 802 " --> pdb=" O   CYS B 810 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL B 800 " --> pdb=" O   ALA B 812 " (cutoff:3.500A)
      removed outlier: 5.603A  pdb=" N   TRP B 837 " --> pdb=" O   ILE B 859 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   GLU B 861 " --> pdb=" O   HIS B 881 " (cutoff:3.500A)

    132 hydrogen bonds defined for protein.
    336 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.97

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2125
        1.34 -     1.46: 1508
        1.46 -     1.58: 2856
        1.58 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 6543
  Sorted by residual:
  bond pdb=" C   PHE A 542 "
       pdb=" N   PRO A 543 "
    ideal  model  delta    sigma   weight residual
    1.337  1.356 -0.019 1.06e-02 8.90e+03 3.24e+00
  bond pdb=" N   PHE A 542 "
       pdb=" CA  PHE A 542 "
    ideal  model  delta    sigma   weight residual
    1.457  1.481 -0.024 1.41e-02 5.03e+03 2.95e+00
  bond pdb=" N   ASN A 541 "
       pdb=" CA  ASN A 541 "
    ideal  model  delta    sigma   weight residual
    1.466  1.487 -0.021 1.51e-02 4.39e+03 1.93e+00
  bond pdb=" N   ILE B 840 "
       pdb=" CA  ILE B 840 "
    ideal  model  delta    sigma   weight residual
    1.459  1.474 -0.015 1.19e-02 7.06e+03 1.62e+00
  bond pdb=" N   ILE A 750 "
       pdb=" CA  ILE A 750 "
    ideal  model  delta    sigma   weight residual
    1.459  1.474 -0.015 1.19e-02 7.06e+03 1.52e+00
  ... (remaining 6538 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 8710
        1.61 -     3.21: 177
        3.21 -     4.82: 12
        4.82 -     6.42: 3
        6.42 -     8.03: 2
  Bond angle restraints: 8904
  Sorted by residual:
  angle pdb=" CA  PHE A 542 "
        pdb=" C   PHE A 542 "
        pdb=" N   PRO A 543 "
      ideal   model   delta    sigma   weight residual
     118.44  126.47   -8.03 1.59e+00 3.96e-01 2.55e+01
  angle pdb=" CA  PHE A 542 "
        pdb=" C   PHE A 542 "
        pdb=" O   PHE A 542 "
      ideal   model   delta    sigma   weight residual
     120.16  114.14    6.02 1.37e+00 5.33e-01 1.93e+01
  angle pdb=" N   PRO A 543 "
        pdb=" CA  PRO A 543 "
        pdb=" C   PRO A 543 "
      ideal   model   delta    sigma   weight residual
     114.27  109.53    4.74 1.35e+00 5.49e-01 1.23e+01
  angle pdb=" C   PHE A 542 "
        pdb=" N   PRO A 543 "
        pdb=" CA  PRO A 543 "
      ideal   model   delta    sigma   weight residual
     120.04  116.43    3.61 1.08e+00 8.57e-01 1.12e+01
  angle pdb=" N   VAL B 827 "
        pdb=" CA  VAL B 827 "
        pdb=" C   VAL B 827 "
      ideal   model   delta    sigma   weight residual
     112.29  109.19    3.10 9.40e-01 1.13e+00 1.08e+01
  ... (remaining 8899 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.40: 3743
       16.40 -    32.79: 111
       32.79 -    49.19: 20
       49.19 -    65.58: 1
       65.58 -    81.98: 3
  Dihedral angle restraints: 3878
    sinusoidal: 1540
      harmonic: 2338
  Sorted by residual:
  dihedral pdb=" CA  SER A 539 "
           pdb=" C   SER A 539 "
           pdb=" N   THR A 540 "
           pdb=" CA  THR A 540 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.25   18.75     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CB  GLU B 952 "
           pdb=" CG  GLU B 952 "
           pdb=" CD  GLU B 952 "
           pdb=" OE1 GLU B 952 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -81.98   81.98     1      3.00e+01 1.11e-03 9.18e+00
  dihedral pdb=" N   TYR A 635 "
           pdb=" CA  TYR A 635 "
           pdb=" CB  TYR A 635 "
           pdb=" CG  TYR A 635 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.96   50.96     3      1.50e+01 4.44e-03 8.96e+00
  ... (remaining 3875 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 561
       0.027 -    0.053: 264
       0.053 -    0.080: 49
       0.080 -    0.107: 63
       0.107 -    0.133: 24
  Chirality restraints: 961
  Sorted by residual:
  chirality pdb=" CA  ASN A 541 "
            pdb=" N   ASN A 541 "
            pdb=" C   ASN A 541 "
            pdb=" CB  ASN A 541 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" CA  ILE A 490 "
            pdb=" N   ILE A 490 "
            pdb=" C   ILE A 490 "
            pdb=" CB  ILE A 490 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CB  VAL A 691 "
            pdb=" CA  VAL A 691 "
            pdb=" CG1 VAL A 691 "
            pdb=" CG2 VAL A 691 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.51   -0.12 2.00e-01 2.50e+01 3.57e-01
  ... (remaining 958 not shown)

  Planarity restraints: 1179
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 540 "   -0.015 2.00e-02 2.50e+03   3.01e-02 9.07e+00
        pdb=" C   THR A 540 "    0.052 2.00e-02 2.50e+03
        pdb=" O   THR A 540 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ASN A 541 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 532 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO A 533 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 533 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 533 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 245 "   -0.017 5.00e-02 4.00e+02   2.60e-02 1.08e+00
        pdb=" N   PRO A 246 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 246 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 246 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1176 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1763
        2.80 -     3.33: 5581
        3.33 -     3.85: 10111
        3.85 -     4.38: 11704
        4.38 -     4.90: 20083
  Nonbonded interactions: 49242
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 848 "
            pdb=" OG  SER B 851 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" OD2 ASP B 874 "
            pdb=" ND2 ASN B 875 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" OD1 ASP A 584 "
            pdb=" OG1 THR A 609 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   PRO A 397 "
            pdb=" NZ  LYS A 483 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" O   ASP A 578 "
            pdb=" OG1 THR A 597 "
     model   vdw
     2.355 3.040
  ... (remaining 49237 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.740
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4185
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      :  0.002   0.025   6557  Z= 0.131
  Angle     :  0.560   8.027   8932  Z= 0.352
  Chirality :  0.040   0.133    961
  Planarity :  0.003   0.034   1179
  Dihedral  :  7.770  81.978   2340
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.79 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  3.67 %
    Favored  : 94.35 %
  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 aren not related in a simple way.
  whole: -3.28 (0.25), residues: 812
  helix: -2.88 (0.47), residues: 50
  sheet: -1.02 (0.34), residues: 196
  loop : -2.74 (0.22), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 807 
 TYR   0.008   0.001   TYR A 276 
 PHE   0.005   0.001   PHE A 693 
 TRP   0.003   0.000   TRP A 255 
 HIS   0.002   0.000   HIS B 881 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 ( 6543)
  covalent geometry    : angle       0.56036 ( 8904)
  SS BOND              : bond        0.00098 (   14)
  SS BOND              : angle       0.39926 (   28)
  hydrogen bonds       : bond        0.28584 (  132)
  hydrogen bonds       : angle      10.77635 (  336)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  529 GLU cc_start: 0.7177 (mp0) cc_final: 0.6077 (tm-30)
REVERT: A  555 ILE cc_start: 0.6198 (mt) cc_final: 0.5975 (tp)
REVERT: A  613 THR cc_start: 0.2966 (m) cc_final: 0.2761 (p)
REVERT: A  620 ASP cc_start: 0.8656 (m-30) cc_final: 0.8426 (m-30)
REVERT: B  809 LEU cc_start: 0.7996 (mt) cc_final: 0.7143 (mt)
REVERT: B  927 ILE cc_start: 0.7961 (mm) cc_final: 0.6967 (mt)
REVERT: B 1004 TYR cc_start: 0.6665 (m-80) cc_final: 0.6327 (m-80)
  outliers start: 14
  outliers final: 5
  residues processed: 135
  average time/residue: 0.0970
  time to fit residues: 16.5693
Evaluate side-chains
  110 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0270
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.6842

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

Flipped N/Q/H residues before XYZ refinement:
A 484 ASN
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 710 GLN
** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 717 GLN
A 766 GLN
B 921 GLN
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 943 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5173 r_free = 0.5173 target = 0.282653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4769 r_free = 0.4769 target = 0.236030 restraints weight = 24405.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4819 r_free = 0.4819 target = 0.241108 restraints weight = 18547.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4854 r_free = 0.4854 target = 0.244828 restraints weight = 14829.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.247158 restraints weight = 12518.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4902 r_free = 0.4902 target = 0.249138 restraints weight = 10902.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.4849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4373
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6557  Z= 0.133
  Angle     :  0.567   9.265   8932  Z= 0.295
  Chirality :  0.044   0.165    961
  Planarity :  0.004   0.038   1179
  Dihedral  :  3.363  27.117    869
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  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 aren not related in a simple way.
  whole: -2.47 (0.27), residues: 812
  helix: -2.08 (0.63), residues: 50
  sheet: -0.63 (0.35), residues: 195
  loop : -2.11 (0.25), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 807 
 TYR   0.011   0.001   TYR B 920 
 PHE   0.014   0.001   PHE B 904 
 TRP   0.016   0.001   TRP B1013 
 HIS   0.005   0.001   HIS A 700 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6543)
  covalent geometry    : angle       0.55711 ( 8904)
  SS BOND              : bond        0.00549 (   14)
  SS BOND              : angle       1.93272 (   28)
  hydrogen bonds       : bond        0.03845 (  132)
  hydrogen bonds       : angle       7.60848 (  336)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  529 GLU cc_start: 0.7103 (mp0) cc_final: 0.6310 (tm-30)
REVERT: A  555 ILE cc_start: 0.6480 (mt) cc_final: 0.6203 (tp)
REVERT: A  620 ASP cc_start: 0.8668 (m-30) cc_final: 0.8371 (m-30)
REVERT: A  647 HIS cc_start: 0.6784 (m-70) cc_final: 0.6460 (m-70)
REVERT: B  808 LEU cc_start: 0.6501 (mt) cc_final: 0.5101 (mt)
REVERT: B  809 LEU cc_start: 0.7620 (mt) cc_final: 0.5830 (mt)
REVERT: B  874 ASP cc_start: 0.7345 (p0) cc_final: 0.6830 (p0)
REVERT: B  942 GLN cc_start: 0.6702 (tp40) cc_final: 0.6452 (tp-100)
REVERT: B  955 ILE cc_start: 0.7699 (tt) cc_final: 0.7351 (pt)
REVERT: B  976 MET cc_start: 0.5688 (mpp) cc_final: 0.5109 (mpp)
REVERT: B 1004 TYR cc_start: 0.6986 (m-80) cc_final: 0.5976 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0991
  time to fit residues: 13.6066
Evaluate side-chains
  95 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0770
   chunk 37 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 41 optimal weight:    0.1980
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:   40.0000
   chunk 12 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.2542

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

Flipped N/Q/H residues before XYZ refinement:
** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 768 ASN
B 875 ASN
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 980 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5109 r_free = 0.5109 target = 0.269775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.217694 restraints weight = 19751.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.223311 restraints weight = 15395.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4734 r_free = 0.4734 target = 0.227608 restraints weight = 12607.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4765 r_free = 0.4765 target = 0.230715 restraints weight = 10673.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4784 r_free = 0.4784 target = 0.232783 restraints weight = 9368.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.4758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4599
moved from start:          0.3541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   6557  Z= 0.200
  Angle     :  0.644   8.821   8932  Z= 0.336
  Chirality :  0.046   0.169    961
  Planarity :  0.004   0.062   1179
  Dihedral  :  4.322  23.944    869
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 16.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.39 %
    Favored  : 96.47 %
  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 aren not related in a simple way.
  whole: -2.17 (0.28), residues: 812
  helix: -1.94 (0.75), residues: 40
  sheet: -0.55 (0.37), residues: 195
  loop : -1.85 (0.25), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 872 
 TYR   0.020   0.002   TYR B 920 
 PHE   0.018   0.002   PHE A 631 
 TRP   0.023   0.002   TRP A 699 
 HIS   0.008   0.001   HIS A 700 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 6543)
  covalent geometry    : angle       0.63613 ( 8904)
  SS BOND              : bond        0.00747 (   14)
  SS BOND              : angle       1.91089 (   28)
  hydrogen bonds       : bond        0.04176 (  132)
  hydrogen bonds       : angle       7.59772 (  336)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  579 VAL cc_start: 0.7158 (m) cc_final: 0.6952 (m)
REVERT: A  620 ASP cc_start: 0.8705 (m-30) cc_final: 0.8350 (m-30)
REVERT: A  661 LEU cc_start: 0.0863 (OUTLIER) cc_final: -0.2037 (mt)
REVERT: A  695 ILE cc_start: 0.4604 (pt) cc_final: 0.3614 (pt)
REVERT: A  764 ARG cc_start: 0.8337 (tpp80) cc_final: 0.7699 (tpp80)
REVERT: B  877 ILE cc_start: 0.7466 (tt) cc_final: 0.7238 (tt)
REVERT: B  884 PHE cc_start: 0.6974 (m-80) cc_final: 0.6622 (m-80)
REVERT: B  954 MET cc_start: 0.7649 (mtp) cc_final: 0.7447 (mtp)
REVERT: B  955 ILE cc_start: 0.7820 (tt) cc_final: 0.6959 (pt)
REVERT: B  984 PHE cc_start: 0.5756 (m-80) cc_final: 0.5511 (m-80)
REVERT: B 1004 TYR cc_start: 0.7221 (m-80) cc_final: 0.5973 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1020
  time to fit residues: 13.8013
Evaluate side-chains
  93 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0770
   chunk 45 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 844 HIS
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 980 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5136 r_free = 0.5136 target = 0.273170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.223217 restraints weight = 21422.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.228876 restraints weight = 16515.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4778 r_free = 0.4778 target = 0.233051 restraints weight = 13455.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4809 r_free = 0.4809 target = 0.235900 restraints weight = 11375.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.238488 restraints weight = 9955.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.4801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4544
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6557  Z= 0.126
  Angle     :  0.556   6.011   8932  Z= 0.289
  Chirality :  0.044   0.153    961
  Planarity :  0.004   0.041   1179
  Dihedral  :  4.063  27.128    869
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  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 aren not related in a simple way.
  whole: -1.83 (0.29), residues: 812
  helix: -1.63 (0.73), residues: 38
  sheet: -0.40 (0.38), residues: 194
  loop : -1.58 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 872 
 TYR   0.010   0.001   TYR B 920 
 PHE   0.013   0.001   PHE A 479 
 TRP   0.011   0.001   TRP B 819 
 HIS   0.002   0.000   HIS B 867 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6543)
  covalent geometry    : angle       0.55068 ( 8904)
  SS BOND              : bond        0.00369 (   14)
  SS BOND              : angle       1.49999 (   28)
  hydrogen bonds       : bond        0.03123 (  132)
  hydrogen bonds       : angle       6.76902 (  336)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  620 ASP cc_start: 0.8680 (m-30) cc_final: 0.8331 (m-30)
REVERT: B  789 SER cc_start: 0.5829 (t) cc_final: 0.5479 (p)
REVERT: B  874 ASP cc_start: 0.7498 (p0) cc_final: 0.7264 (p0)
REVERT: B  877 ILE cc_start: 0.7572 (tt) cc_final: 0.7363 (tt)
REVERT: B  884 PHE cc_start: 0.6955 (m-80) cc_final: 0.6601 (m-80)
REVERT: B  908 ARG cc_start: 0.4717 (mtp180) cc_final: 0.4441 (mtp180)
REVERT: B  954 MET cc_start: 0.7483 (mtp) cc_final: 0.7238 (mtp)
REVERT: B  976 MET cc_start: 0.5916 (mpp) cc_final: 0.5302 (mpp)
REVERT: B  984 PHE cc_start: 0.5439 (m-80) cc_final: 0.5153 (m-80)
REVERT: B 1004 TYR cc_start: 0.7314 (m-80) cc_final: 0.5949 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1067
  time to fit residues: 14.1540
Evaluate side-chains
  96 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 50 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 0 optimal weight:   60.0000
   chunk 2 optimal weight:    0.0970
   chunk 79 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 980 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5136 r_free = 0.5136 target = 0.274345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.221227 restraints weight = 20500.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.226774 restraints weight = 15878.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4764 r_free = 0.4764 target = 0.231136 restraints weight = 13004.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4795 r_free = 0.4795 target = 0.234265 restraints weight = 11015.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4819 r_free = 0.4819 target = 0.237069 restraints weight = 9681.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.4787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4554
moved from start:          0.4122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6557  Z= 0.124
  Angle     :  0.550   7.162   8932  Z= 0.287
  Chirality :  0.044   0.143    961
  Planarity :  0.004   0.039   1179
  Dihedral  :  3.998  26.625    869
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  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 aren not related in a simple way.
  whole: -1.73 (0.29), residues: 812
  helix: -1.50 (0.74), residues: 38
  sheet: -0.39 (0.38), residues: 201
  loop : -1.50 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 872 
 TYR   0.009   0.001   TYR B 804 
 PHE   0.009   0.001   PHE A 452 
 TRP   0.015   0.001   TRP A 699 
 HIS   0.005   0.001   HIS A 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6543)
  covalent geometry    : angle       0.54310 ( 8904)
  SS BOND              : bond        0.00554 (   14)
  SS BOND              : angle       1.64728 (   28)
  hydrogen bonds       : bond        0.02999 (  132)
  hydrogen bonds       : angle       6.45162 (  336)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  555 ILE cc_start: 0.5974 (mp) cc_final: 0.5644 (mp)
REVERT: A  620 ASP cc_start: 0.8663 (m-30) cc_final: 0.8400 (m-30)
REVERT: B  789 SER cc_start: 0.5863 (t) cc_final: 0.5467 (p)
REVERT: B  872 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8250 (mmm160)
REVERT: B  884 PHE cc_start: 0.6941 (m-80) cc_final: 0.6586 (m-80)
REVERT: B  908 ARG cc_start: 0.4909 (mtp180) cc_final: 0.4601 (mtp180)
REVERT: B  976 MET cc_start: 0.5902 (mpp) cc_final: 0.5296 (mpp)
REVERT: B 1004 TYR cc_start: 0.7281 (m-80) cc_final: 0.5917 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1010
  time to fit residues: 12.8309
Evaluate side-chains
  92 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0670
   chunk 46 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.1924

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

Flipped N/Q/H residues before XYZ refinement:
A 480 ASN
A 541 ASN
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 867 HIS
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 980 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5091 r_free = 0.5091 target = 0.268358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.208339 restraints weight = 18273.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.211878 restraints weight = 15715.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.214506 restraints weight = 13853.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.216459 restraints weight = 12609.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.217792 restraints weight = 11775.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.4664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4890
moved from start:          0.4922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6557  Z= 0.181
  Angle     :  0.635   6.403   8932  Z= 0.332
  Chirality :  0.046   0.171    961
  Planarity :  0.004   0.047   1179
  Dihedral  :  4.565  26.132    869
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.61 %
    Favored  : 90.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  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 aren not related in a simple way.
  whole: -1.78 (0.30), residues: 812
  helix: -1.87 (0.69), residues: 40
  sheet: -0.73 (0.37), residues: 211
  loop : -1.36 (0.27), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 982 
 TYR   0.012   0.001   TYR B 920 
 PHE   0.016   0.002   PHE B 984 
 TRP   0.015   0.002   TRP A 707 
 HIS   0.007   0.001   HIS A 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 6543)
  covalent geometry    : angle       0.62716 ( 8904)
  SS BOND              : bond        0.00819 (   14)
  SS BOND              : angle       1.83121 (   28)
  hydrogen bonds       : bond        0.03676 (  132)
  hydrogen bonds       : angle       6.94527 (  336)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  620 ASP cc_start: 0.8549 (m-30) cc_final: 0.8273 (m-30)
REVERT: B  789 SER cc_start: 0.5696 (t) cc_final: 0.5322 (p)
REVERT: B  831 ASN cc_start: 0.8106 (p0) cc_final: 0.7747 (t0)
REVERT: B  864 ILE cc_start: 0.8318 (mm) cc_final: 0.7549 (tt)
REVERT: B  877 ILE cc_start: 0.7682 (tt) cc_final: 0.7445 (tt)
REVERT: B  884 PHE cc_start: 0.7074 (m-80) cc_final: 0.6640 (m-80)
REVERT: B  954 MET cc_start: 0.7248 (mtp) cc_final: 0.6951 (ttm)
REVERT: B  976 MET cc_start: 0.5780 (mpp) cc_final: 0.5090 (mpp)
REVERT: B  981 ASN cc_start: 0.8306 (t0) cc_final: 0.8010 (t0)
REVERT: B  982 ARG cc_start: 0.6548 (mtp180) cc_final: 0.6073 (mtp85)
REVERT: B 1004 TYR cc_start: 0.7215 (m-80) cc_final: 0.5980 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1076
  time to fit residues: 13.1439
Evaluate side-chains
  85 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 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 = 0.5095 r_free = 0.5095 target = 0.268227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.208815 restraints weight = 17956.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.212211 restraints weight = 15274.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.214997 restraints weight = 13507.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.216391 restraints weight = 12214.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4712 r_free = 0.4712 target = 0.218449 restraints weight = 11508.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.4675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4860
moved from start:          0.5224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   6557  Z= 0.162
  Angle     :  0.611   8.150   8932  Z= 0.318
  Chirality :  0.045   0.156    961
  Planarity :  0.004   0.048   1179
  Dihedral  :  4.534  27.277    869
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.73 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  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 aren not related in a simple way.
  whole: -1.81 (0.30), residues: 812
  helix: -1.61 (0.72), residues: 38
  sheet: -0.54 (0.38), residues: 200
  loop : -1.50 (0.27), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 872 
 TYR   0.016   0.001   TYR B 959 
 PHE   0.021   0.002   PHE A 693 
 TRP   0.012   0.001   TRP B 819 
 HIS   0.007   0.001   HIS A 700 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6543)
  covalent geometry    : angle       0.60523 ( 8904)
  SS BOND              : bond        0.00520 (   14)
  SS BOND              : angle       1.61866 (   28)
  hydrogen bonds       : bond        0.03361 (  132)
  hydrogen bonds       : angle       6.76717 (  336)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: A  620 ASP cc_start: 0.8567 (m-30) cc_final: 0.8227 (m-30)
REVERT: B  789 SER cc_start: 0.5810 (t) cc_final: 0.5403 (p)
REVERT: B  863 VAL cc_start: 0.7533 (t) cc_final: 0.7257 (t)
REVERT: B  864 ILE cc_start: 0.8327 (mm) cc_final: 0.7574 (tt)
REVERT: B  868 TYR cc_start: 0.6842 (t80) cc_final: 0.6601 (t80)
REVERT: B  877 ILE cc_start: 0.7656 (tt) cc_final: 0.7425 (tt)
REVERT: B  884 PHE cc_start: 0.7119 (m-80) cc_final: 0.6664 (m-80)
REVERT: B  976 MET cc_start: 0.5829 (mpp) cc_final: 0.5218 (mpp)
REVERT: B  981 ASN cc_start: 0.8550 (t0) cc_final: 0.8269 (t0)
REVERT: B 1004 TYR cc_start: 0.7267 (m-80) cc_final: 0.6123 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1141
  time to fit residues: 14.3509
Evaluate side-chains
  86 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0980
   chunk 78 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0870
   chunk 80 optimal weight:    0.0370
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.3036

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 565 GLN
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 875 ASN
** B 929 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 = 0.5128 r_free = 0.5128 target = 0.272086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.225776 restraints weight = 20700.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.231080 restraints weight = 16210.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4793 r_free = 0.4793 target = 0.235214 restraints weight = 13148.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4821 r_free = 0.4821 target = 0.237983 restraints weight = 11091.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.240480 restraints weight = 9623.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.4818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4551
moved from start:          0.5230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   6557  Z= 0.107
  Angle     :  0.579   8.198   8932  Z= 0.299
  Chirality :  0.044   0.148    961
  Planarity :  0.004   0.063   1179
  Dihedral  :  4.284  28.949    869
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  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 aren not related in a simple way.
  whole: -1.68 (0.30), residues: 812
  helix: -1.07 (0.78), residues: 39
  sheet: -0.49 (0.37), residues: 204
  loop : -1.43 (0.27), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 872 
 TYR   0.009   0.001   TYR A 458 
 PHE   0.018   0.001   PHE B 991 
 TRP   0.023   0.002   TRP B 915 
 HIS   0.005   0.001   HIS A 435 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 6543)
  covalent geometry    : angle       0.57655 ( 8904)
  SS BOND              : bond        0.00231 (   14)
  SS BOND              : angle       1.16025 (   28)
  hydrogen bonds       : bond        0.02873 (  132)
  hydrogen bonds       : angle       6.13445 (  336)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  620 ASP cc_start: 0.8534 (m-30) cc_final: 0.8257 (m-30)
REVERT: B  789 SER cc_start: 0.5904 (t) cc_final: 0.5546 (p)
REVERT: B  874 ASP cc_start: 0.7580 (p0) cc_final: 0.7120 (p0)
REVERT: B  884 PHE cc_start: 0.6880 (m-80) cc_final: 0.6500 (m-80)
REVERT: B  908 ARG cc_start: 0.5545 (mtt180) cc_final: 0.5006 (mtt180)
REVERT: B  954 MET cc_start: 0.7205 (mtp) cc_final: 0.6992 (mtp)
REVERT: B  976 MET cc_start: 0.6321 (mpp) cc_final: 0.5736 (mpp)
REVERT: B  981 ASN cc_start: 0.8326 (t0) cc_final: 0.8078 (t0)
REVERT: B 1004 TYR cc_start: 0.7283 (m-80) cc_final: 0.6107 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1150
  time to fit residues: 13.5490
Evaluate side-chains
  90 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 0 optimal weight:   60.0000
   chunk 22 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 49 optimal weight:    0.5980
   chunk 55 optimal weight:    0.4980
   chunk 14 optimal weight:    5.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 980 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5086 r_free = 0.5086 target = 0.267426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.205861 restraints weight = 18570.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.207986 restraints weight = 15869.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.212314 restraints weight = 14267.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.214931 restraints weight = 12769.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.215843 restraints weight = 11697.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.4649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4974
moved from start:          0.5764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6557  Z= 0.194
  Angle     :  0.655   7.362   8932  Z= 0.343
  Chirality :  0.046   0.174    961
  Planarity :  0.005   0.054   1179
  Dihedral  :  4.690  27.633    869
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 18.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.61 %
    Favored  : 90.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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 aren not related in a simple way.
  whole: -1.83 (0.29), residues: 812
  helix: -1.82 (0.69), residues: 40
  sheet: -0.54 (0.38), residues: 204
  loop : -1.51 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 679 
 TYR   0.015   0.002   TYR B 959 
 PHE   0.018   0.002   PHE B 991 
 TRP   0.019   0.002   TRP A 707 
 HIS   0.006   0.001   HIS A 700 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 6543)
  covalent geometry    : angle       0.64804 ( 8904)
  SS BOND              : bond        0.00657 (   14)
  SS BOND              : angle       1.77030 (   28)
  hydrogen bonds       : bond        0.03539 (  132)
  hydrogen bonds       : angle       6.81718 (  336)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  565 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7247 (tm-30)
REVERT: A  620 ASP cc_start: 0.8545 (m-30) cc_final: 0.8312 (m-30)
REVERT: B  789 SER cc_start: 0.5884 (t) cc_final: 0.5436 (p)
REVERT: B  809 LEU cc_start: 0.8124 (mt) cc_final: 0.7269 (mt)
REVERT: B  819 TRP cc_start: 0.4185 (m100) cc_final: 0.3709 (m100)
REVERT: B  872 ARG cc_start: 0.8397 (mmm160) cc_final: 0.7642 (mmm-85)
REVERT: B  874 ASP cc_start: 0.7478 (p0) cc_final: 0.7042 (p0)
REVERT: B  884 PHE cc_start: 0.7242 (m-80) cc_final: 0.6789 (m-80)
REVERT: B  908 ARG cc_start: 0.5905 (mtt180) cc_final: 0.5335 (mtt180)
REVERT: B  953 ASN cc_start: 0.4741 (m-40) cc_final: 0.4463 (m-40)
REVERT: B  976 MET cc_start: 0.5691 (mpp) cc_final: 0.5075 (mpp)
REVERT: B  981 ASN cc_start: 0.8627 (t0) cc_final: 0.8410 (t0)
REVERT: B 1004 TYR cc_start: 0.7019 (m-80) cc_final: 0.5930 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1031
  time to fit residues: 13.0192
Evaluate side-chains
  92 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 0 optimal weight:  100.0000
   chunk 1 optimal weight:    8.9990
   chunk 77 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 57 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 384 HIS
** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 725 ASN
** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 980 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5016 r_free = 0.5016 target = 0.256590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.191137 restraints weight = 16271.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.195108 restraints weight = 14403.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.197001 restraints weight = 12726.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.200490 restraints weight = 11731.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.201481 restraints weight = 10745.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.4517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5167
moved from start:          0.6913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.087   6557  Z= 0.340
  Angle     :  0.889  10.586   8932  Z= 0.474
  Chirality :  0.052   0.249    961
  Planarity :  0.007   0.141   1179
  Dihedral  :  6.043  27.680    869
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 29.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.95 %
    Favored  : 88.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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 aren not related in a simple way.
  whole: -2.34 (0.28), residues: 812
  helix: -2.24 (0.67), residues: 41
  sheet: -0.47 (0.41), residues: 178
  loop : -2.00 (0.24), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.002   ARG A 694 
 TYR   0.036   0.002   TYR B 804 
 PHE   0.027   0.002   PHE A 693 
 TRP   0.048   0.004   TRP A 707 
 HIS   0.015   0.002   HIS A 700 

Details of bonding type rmsd
  covalent geometry    : bond        0.00729 ( 6543)
  covalent geometry    : angle       0.88070 ( 8904)
  SS BOND              : bond        0.00804 (   14)
  SS BOND              : angle       2.38857 (   28)
  hydrogen bonds       : bond        0.05332 (  132)
  hydrogen bonds       : angle       8.61566 (  336)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.227 
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  620 ASP cc_start: 0.8739 (m-30) cc_final: 0.8519 (m-30)
REVERT: A  770 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7832 (mtpp)
REVERT: B  809 LEU cc_start: 0.8200 (mt) cc_final: 0.7829 (mt)
REVERT: B  819 TRP cc_start: 0.4490 (m100) cc_final: 0.3943 (m100)
REVERT: B  872 ARG cc_start: 0.8530 (mmm160) cc_final: 0.7704 (mmm-85)
REVERT: B  874 ASP cc_start: 0.7649 (p0) cc_final: 0.7437 (p0)
REVERT: B  877 ILE cc_start: 0.7578 (tt) cc_final: 0.7051 (tt)
REVERT: B  884 PHE cc_start: 0.7330 (m-80) cc_final: 0.6905 (m-80)
REVERT: B  982 ARG cc_start: 0.5745 (mtp180) cc_final: 0.5335 (mtp180)
REVERT: B  989 THR cc_start: 0.7896 (m) cc_final: 0.6196 (m)
REVERT: B 1004 TYR cc_start: 0.6852 (m-80) cc_final: 0.5933 (m-80)
REVERT: B 1010 PHE cc_start: 0.7099 (m-80) cc_final: 0.6437 (m-80)
REVERT: B 1014 ILE cc_start: 0.7843 (mt) cc_final: 0.7635 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0895
  time to fit residues: 11.6954
Evaluate side-chains
  89 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0970
   chunk 33 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0980
   chunk 63 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 534 ASN
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 881 HIS
** B 929 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 = 0.5099 r_free = 0.5099 target = 0.269272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.214653 restraints weight = 18317.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.219843 restraints weight = 14682.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.224012 restraints weight = 12194.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4724 r_free = 0.4724 target = 0.227250 restraints weight = 10457.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.229427 restraints weight = 9219.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.4697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4746
moved from start:          0.6733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6557  Z= 0.129
  Angle     :  0.639   7.820   8932  Z= 0.334
  Chirality :  0.045   0.143    961
  Planarity :  0.004   0.047   1179
  Dihedral  :  4.962  29.551    869
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 17.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 aren not related in a simple way.
  whole: -1.99 (0.29), residues: 812
  helix: -1.65 (0.72), residues: 41
  sheet: -0.80 (0.39), residues: 190
  loop : -1.57 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 872 
 TYR   0.008   0.001   TYR B1004 
 PHE   0.014   0.002   PHE B 991 
 TRP   0.019   0.002   TRP B 819 
 HIS   0.006   0.001   HIS A 700 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6543)
  covalent geometry    : angle       0.63448 ( 8904)
  SS BOND              : bond        0.00308 (   14)
  SS BOND              : angle       1.43944 (   28)
  hydrogen bonds       : bond        0.03125 (  132)
  hydrogen bonds       : angle       7.15799 (  336)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1604.71 seconds
wall clock time: 28 minutes 15.84 seconds (1695.84 seconds total)