Starting phenix.real_space_refine
on Sun May 11 06:01:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r4b_18884/05_2025/8r4b_18884_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r4b_18884/05_2025/8r4b_18884.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r4b_18884/05_2025/8r4b_18884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r4b_18884/05_2025/8r4b_18884.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r4b_18884/05_2025/8r4b_18884_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r4b_18884/05_2025/8r4b_18884_neut.cif"
  }
  resolution = 3.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002 sd=   0.063
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      24      5.16       5
     C    4806      2.51       5
     N    1277      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7600
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 808, 5956
          Classifications: {'peptide': 808}
          Incomplete info: {'truncation_to_alanine': 114}
          Link IDs: {'PTRANS': 34, 'TRANS': 773}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 415
          Unresolved non-hydrogen angles: 499
          Unresolved non-hydrogen dihedrals: 343
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 209
    Chain: "B"
      Number of atoms: 769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 769
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 3, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 80
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 48
    Chain: "C"
      Number of atoms: 843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 843
          Classifications: {'peptide': 116}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 3, 'TRANS': 112}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GSP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.95, per 1000 atoms: 0.65
  Number of scatterers: 7600
  At special positions: 0
  Unit cell: (70.97, 80.03, 182.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P       3     15.00
     O    1490      8.00
     N    1277      7.00
     C    4806      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " 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: 2.10
  Conformation dependent library (CDL) restraints added in 971.6 milliseconds
  

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1952

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 11 sheets defined
      24.5% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 15
    Processing helix  chain 'A' and resid 51 through 62
      removed outlier: 3.736A  pdb=" N   ILE A  56 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   GLN A  57 " --> pdb=" O   ASP A  53 " (cutoff:3.500A)
      Proline residue:  A  58  - end of helix
      removed outlier: 3.617A  pdb=" N   LEU A  62 " --> pdb=" O   PRO A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 127
      removed outlier: 4.089A  pdb=" N   SER A 127 " --> pdb=" O   PRO A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 150
      removed outlier: 3.522A  pdb=" N   SER A 149 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 172
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 4.089A  pdb=" N   GLU A 214 " --> pdb=" O   ALA A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 3.904A  pdb=" N   SER A 237 " --> pdb=" O   PRO A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 260
    Processing helix  chain 'A' and resid 298 through 302
    Processing helix  chain 'A' and resid 320 through 324
    Processing helix  chain 'A' and resid 342 through 346
      removed outlier: 3.740A  pdb=" N   LEU A 345 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 392
    Processing helix  chain 'A' and resid 419 through 426
      removed outlier: 3.790A  pdb=" N   GLY A 426 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 439
    Processing helix  chain 'A' and resid 465 through 470
    Processing helix  chain 'A' and resid 503 through 507
      removed outlier: 3.834A  pdb=" N   LEU A 506 " --> pdb=" O   ASP A 503 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LYS A 507 " --> pdb=" O   ASP A 504 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 503 through 507'
    Processing helix  chain 'A' and resid 541 through 545
      removed outlier: 3.631A  pdb=" N   ASP A 545 " --> pdb=" O   SER A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 558
      removed outlier: 3.626A  pdb=" N   LEU A 552 " --> pdb=" O   LYS A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 588
    Processing helix  chain 'A' and resid 608 through 618
      removed outlier: 3.512A  pdb=" N   LEU A 618 " --> pdb=" O   LYS A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 647
      removed outlier: 3.629A  pdb=" N   ILE A 633 " --> pdb=" O   ALA A 629 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ALA A 645 " --> pdb=" O   GLU A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 661
      removed outlier: 4.040A  pdb=" N   SER A 661 " --> pdb=" O   ILE A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 678
    Processing helix  chain 'A' and resid 697 through 710
      removed outlier: 3.551A  pdb=" N   THR A 702 " --> pdb=" O   PRO A 698 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   ILE A 703 " --> pdb=" O   HIS A 699 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   VAL A 705 " --> pdb=" O   VAL A 701 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASN A 710 " --> pdb=" O   TYR A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 728
      removed outlier: 3.687A  pdb=" N   ILE A 727 " --> pdb=" O   ALA A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 763
    Processing helix  chain 'A' and resid 809 through 814
    Processing helix  chain 'A' and resid 872 through 881
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.849A  pdb=" N   THR C  90 " --> pdb=" O   PRO C  87 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20
      removed outlier: 6.298A  pdb=" N   GLU A  19 " --> pdb=" O   TYR A  31 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLY A  30 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ALA A  41 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LEU A 222 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267
      removed outlier: 6.842A  pdb=" N   LEU A 310 " --> pdb=" O   TRP A 333 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 377
      removed outlier: 6.411A  pdb=" N   GLU A 396 " --> pdb=" O   ILE A 408 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 490 through 493
      removed outlier: 8.611A  pdb=" N   VAL A 535 " --> pdb=" O   GLU A 452 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   LYS A 454 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   MET A 537 " --> pdb=" O   LYS A 454 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   HIS A 456 " --> pdb=" O   MET A 537 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   LEU A 539 " --> pdb=" O   HIS A 456 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ILE A 458 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      removed outlier: 8.610A  pdb=" N   ILE A 565 " --> pdb=" O   SER A 534 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   TYR A 536 " --> pdb=" O   ILE A 565 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   VAL A 567 " --> pdb=" O   TYR A 536 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   LEU A 538 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   HIS A 596 " --> pdb=" O   VAL A 566 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 830 through 834
      removed outlier: 3.622A  pdb=" N   LYS A 844 " --> pdb=" O   ALA A 857 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   MET A 800 " --> pdb=" O   ILE A 854 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 23
    Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.839A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54
    Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 11
      removed outlier: 6.184A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   VAL C  33 " --> pdb=" O   ASP C  98 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   MET C  34 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   SER C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11
      removed outlier: 6.184A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   GLY C  99 " --> pdb=" O   ASN C 107 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   ASN C 107 " --> pdb=" O   GLY C  99 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   ILE C 101 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   TYR C 105 " --> pdb=" O   ILE C 101 " (cutoff:3.500A)

    237 hydrogen bonds defined for protein.
    597 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: 2.79

  Time building geometry restraints manager: 2.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2494
        1.34 -     1.46: 1166
        1.46 -     1.57: 4028
        1.57 -     1.69: 5
        1.69 -     1.81: 38
  Bond restraints: 7731
  Sorted by residual:
  bond pdb=" N   GLU A 769 "
       pdb=" CA  GLU A 769 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.67e+00
  bond pdb=" N   PRO A 414 "
       pdb=" CA  PRO A 414 "
    ideal  model  delta    sigma   weight residual
    1.469  1.485 -0.016 1.28e-02 6.10e+03 1.57e+00
  bond pdb=" C   ALA B  40 "
       pdb=" N   PRO B  41 "
    ideal  model  delta    sigma   weight residual
    1.340  1.373 -0.033 2.76e-02 1.31e+03 1.46e+00
  bond pdb=" CB  ILE A 144 "
       pdb=" CG1 ILE A 144 "
    ideal  model  delta    sigma   weight residual
    1.530  1.554 -0.024 2.00e-02 2.50e+03 1.39e+00
  bond pdb=" CA  ILE A 144 "
       pdb=" CB  ILE A 144 "
    ideal  model  delta    sigma   weight residual
    1.540  1.556 -0.016 1.36e-02 5.41e+03 1.36e+00
  ... (remaining 7726 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 10144
        1.54 -     3.08: 321
        3.08 -     4.62: 65
        4.62 -     6.16: 18
        6.16 -     7.70: 6
  Bond angle restraints: 10554
  Sorted by residual:
  angle pdb=" N   ILE A 166 "
        pdb=" CA  ILE A 166 "
        pdb=" C   ILE A 166 "
      ideal   model   delta    sigma   weight residual
     113.20  109.25    3.95 9.60e-01 1.09e+00 1.69e+01
  angle pdb=" CB  ILE A 144 "
        pdb=" CG1 ILE A 144 "
        pdb=" CD1 ILE A 144 "
      ideal   model   delta    sigma   weight residual
     113.80  121.50   -7.70 2.10e+00 2.27e-01 1.34e+01
  angle pdb=" CA  ILE A 144 "
        pdb=" CB  ILE A 144 "
        pdb=" CG1 ILE A 144 "
      ideal   model   delta    sigma   weight residual
     110.40  116.37   -5.97 1.70e+00 3.46e-01 1.23e+01
  angle pdb=" CA  GLN A  12 "
        pdb=" CB  GLN A  12 "
        pdb=" CG  GLN A  12 "
      ideal   model   delta    sigma   weight residual
     114.10  120.43   -6.33 2.00e+00 2.50e-01 1.00e+01
  angle pdb=" N   ALA C  91 "
        pdb=" CA  ALA C  91 "
        pdb=" C   ALA C  91 "
      ideal   model   delta    sigma   weight residual
     108.34  112.10   -3.76 1.31e+00 5.83e-01 8.24e+00
  ... (remaining 10549 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.03: 4185
       22.03 -    44.05: 394
       44.05 -    66.08: 46
       66.08 -    88.11: 12
       88.11 -   110.14: 2
  Dihedral angle restraints: 4639
    sinusoidal: 1637
      harmonic: 3002
  Sorted by residual:
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  95 "
           pdb=" CB  CYS C  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.81  -74.81     1      1.00e+01 1.00e-02 7.09e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  99 "
           pdb=" CB  CYS B  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.71  -48.71     1      1.00e+01 1.00e-02 3.27e+01
  dihedral pdb=" O3B GSP A1201 "
           pdb=" O3A GSP A1201 "
           pdb=" PB  GSP A1201 "
           pdb=" PA  GSP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.55 -156.31 -110.14     1      2.00e+01 2.50e-03 3.23e+01
  ... (remaining 4636 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 768
       0.033 -    0.067: 354
       0.067 -    0.100: 105
       0.100 -    0.133: 40
       0.133 -    0.167: 4
  Chirality restraints: 1271
  Sorted by residual:
  chirality pdb=" CA  ILE A 821 "
            pdb=" N   ILE A 821 "
            pdb=" C   ILE A 821 "
            pdb=" CB  ILE A 821 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.94e-01
  chirality pdb=" CA  ILE A 408 "
            pdb=" N   ILE A 408 "
            pdb=" C   ILE A 408 "
            pdb=" CB  ILE A 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.82e-01
  chirality pdb=" CA  ILE A 565 "
            pdb=" N   ILE A 565 "
            pdb=" C   ILE A 565 "
            pdb=" CB  ILE A 565 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  ... (remaining 1268 not shown)

  Planarity restraints: 1346
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 413 "    0.031 5.00e-02 4.00e+02   4.71e-02 3.54e+00
        pdb=" N   PRO A 414 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 414 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 414 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 189 "   -0.030 5.00e-02 4.00e+02   4.52e-02 3.27e+00
        pdb=" N   PRO A 190 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 190 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 190 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 803 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.71e+00
        pdb=" CG  ASP A 803 "    0.028 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 803 "   -0.010 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 803 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1343 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 701
        2.75 -     3.28: 7503
        3.28 -     3.82: 12321
        3.82 -     4.36: 14678
        4.36 -     4.90: 24858
  Nonbonded interactions: 60061
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  45 "
            pdb=" OD1 ASN C  32 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   SER A 417 "
            pdb=" OH  TYR A 433 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG1 THR A 154 "
            pdb=" OE1 GLU A 155 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   SER A 352 "
            pdb=" OG1 THR A 374 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" N   GLU A 686 "
            pdb=" OE1 GLU A 686 "
     model   vdw
     2.289 3.120
  ... (remaining 60056 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:             0.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.960
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6838
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7733  Z= 0.145
  Angle     :  0.686   7.697  10558  Z= 0.365
  Chirality :  0.044   0.167   1271
  Planarity :  0.005   0.047   1346
  Dihedral  : 16.622 110.136   2681
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.51 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 20.63 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.25), residues: 1009
  helix: -1.10 (0.34), residues: 233
  sheet: -1.20 (0.32), residues: 250
  loop : -2.57 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP C  36 
 HIS   0.004   0.001   HIS A 549 
 PHE   0.014   0.001   PHE A 410 
 TYR   0.011   0.001   TYR C  37 
 ARG   0.007   0.001   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14884 (  233)
  hydrogen bonds       : angle       6.61955 (  597)
  SS BOND              : bond        0.00372 (    2)
  SS BOND              : angle       1.42580 (    4)
  covalent geometry    : bond        0.00322 ( 7731)
  covalent geometry    : angle       0.68603 (10554)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 228
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7587 (tt0)
REVERT: A  252 THR cc_start: 0.7969 (p) cc_final: 0.7747 (m)
REVERT: A  275 ASP cc_start: 0.6974 (t0) cc_final: 0.6558 (t0)
REVERT: A  323 LEU cc_start: 0.7940 (tp) cc_final: 0.7739 (mm)
REVERT: A  351 LEU cc_start: 0.8182 (mt) cc_final: 0.7940 (mt)
REVERT: A  402 PHE cc_start: 0.6348 (t80) cc_final: 0.6051 (t80)
REVERT: A  409 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.7958 (p)
REVERT: A  427 LYS cc_start: 0.7390 (tmtt) cc_final: 0.6904 (tttp)
REVERT: A  432 GLN cc_start: 0.8751 (mt0) cc_final: 0.8031 (mm-40)
REVERT: A  706 TYR cc_start: 0.3964 (t80) cc_final: 0.2587 (t80)
REVERT: A  715 LYS cc_start: 0.8547 (tttt) cc_final: 0.8291 (tptt)
REVERT: A  753 GLN cc_start: 0.6659 (tt0) cc_final: 0.6411 (tt0)
REVERT: B   86 MET cc_start: 0.7352 (mmm) cc_final: 0.6425 (mmp)
REVERT: C   12 VAL cc_start: 0.7922 (t) cc_final: 0.7583 (p)
REVERT: C   45 ARG cc_start: 0.7138 (mtm-85) cc_final: 0.6855 (mtt180)
REVERT: C   56 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7201 (mtm180)
REVERT: C   80 LEU cc_start: 0.8706 (tp) cc_final: 0.8222 (tp)
REVERT: C  114 THR cc_start: 0.8573 (m) cc_final: 0.8340 (p)
  outliers start: 4
  outliers final: 1
  residues processed: 230
  average time/residue: 0.1783
  time to fit residues: 55.5702
Evaluate side-chains
  188 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  577 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0070
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0970
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 HIS
A 819 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.112896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.098334 restraints weight = 16062.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.100279 restraints weight = 10424.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.101712 restraints weight = 7590.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7733  Z= 0.163
  Angle     :  0.681  10.089  10558  Z= 0.350
  Chirality :  0.045   0.247   1271
  Planarity :  0.005   0.040   1346
  Dihedral  :  7.659 107.106   1094
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.81 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 20.63 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.25), residues: 1009
  helix: -1.10 (0.34), residues: 231
  sheet: -1.21 (0.32), residues: 237
  loop : -2.50 (0.24), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  36 
 HIS   0.012   0.002   HIS A 449 
 PHE   0.026   0.002   PHE A 410 
 TYR   0.019   0.002   TYR C  94 
 ARG   0.006   0.001   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04045 (  233)
  hydrogen bonds       : angle       5.30652 (  597)
  SS BOND              : bond        0.00457 (    2)
  SS BOND              : angle       1.54243 (    4)
  covalent geometry    : bond        0.00382 ( 7731)
  covalent geometry    : angle       0.68025 (10554)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 198
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.8076 (p0) cc_final: 0.7787 (p0)
REVERT: A  131 LEU cc_start: 0.8118 (tp) cc_final: 0.7772 (tt)
REVERT: A  147 LEU cc_start: 0.8803 (mp) cc_final: 0.8548 (mm)
REVERT: A  184 GLN cc_start: 0.7786 (mp10) cc_final: 0.7570 (mp10)
REVERT: A  252 THR cc_start: 0.8170 (p) cc_final: 0.7941 (m)
REVERT: A  275 ASP cc_start: 0.7118 (t0) cc_final: 0.6880 (t0)
REVERT: A  323 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7749 (mm)
REVERT: A  402 PHE cc_start: 0.6342 (t80) cc_final: 0.6069 (t80)
REVERT: A  409 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.7706 (p)
REVERT: A  427 LYS cc_start: 0.7293 (tmtt) cc_final: 0.6890 (tttp)
REVERT: A  432 GLN cc_start: 0.8814 (mt0) cc_final: 0.8215 (mm110)
REVERT: A  547 ASN cc_start: 0.6252 (t0) cc_final: 0.5995 (t0)
REVERT: A  574 ASN cc_start: 0.7933 (t0) cc_final: 0.7654 (t0)
REVERT: A  696 LEU cc_start: 0.5150 (OUTLIER) cc_final: 0.4826 (pt)
REVERT: A  715 LYS cc_start: 0.8810 (tttt) cc_final: 0.8425 (tptt)
REVERT: B   86 MET cc_start: 0.7117 (mmm) cc_final: 0.6599 (mmm)
REVERT: C   45 ARG cc_start: 0.6760 (mtm-85) cc_final: 0.6372 (mtt180)
REVERT: C   56 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7264 (mtm180)
REVERT: C   66 ARG cc_start: 0.7080 (mtm-85) cc_final: 0.6846 (mtp-110)
REVERT: C   80 LEU cc_start: 0.8591 (tp) cc_final: 0.8237 (tp)
REVERT: C  114 THR cc_start: 0.8490 (m) cc_final: 0.8198 (p)
  outliers start: 47
  outliers final: 23
  residues processed: 220
  average time/residue: 0.1686
  time to fit residues: 50.9503
Evaluate side-chains
  201 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 174
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   79 SER
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  526 HIS
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  650 ASN
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   56 ARG
Chi-restraints excluded: chain C residue   57 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0980
   chunk 62 optimal weight:    0.4980
   chunk 81 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0980
   chunk 29 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 316 GLN
A 578 ASN
A 819 HIS
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.111569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.096700 restraints weight = 16323.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.098845 restraints weight = 10400.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.100359 restraints weight = 7425.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7733  Z= 0.157
  Angle     :  0.665   7.758  10558  Z= 0.339
  Chirality :  0.045   0.257   1271
  Planarity :  0.004   0.041   1346
  Dihedral  :  7.661 108.132   1094
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  8.72 %
    Favored  : 90.88 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 22.72 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.65 (0.25), residues: 1009
  helix: -1.11 (0.34), residues: 241
  sheet: -1.10 (0.33), residues: 237
  loop : -2.43 (0.25), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  36 
 HIS   0.010   0.001   HIS A 523 
 PHE   0.018   0.002   PHE A 410 
 TYR   0.013   0.001   TYR C  94 
 ARG   0.003   0.001   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04132 (  233)
  hydrogen bonds       : angle       5.19238 (  597)
  SS BOND              : bond        0.00394 (    2)
  SS BOND              : angle       1.48697 (    4)
  covalent geometry    : bond        0.00369 ( 7731)
  covalent geometry    : angle       0.66426 (10554)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 201
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ASP cc_start: 0.5922 (p0) cc_final: 0.5187 (p0)
REVERT: A   38 ARG cc_start: 0.6857 (mpt-90) cc_final: 0.6652 (mmt90)
REVERT: A   54 ARG cc_start: 0.7810 (ptp90) cc_final: 0.7132 (ptt-90)
REVERT: A   85 ASN cc_start: 0.7965 (p0) cc_final: 0.7707 (p0)
REVERT: A   86 SER cc_start: 0.8014 (p) cc_final: 0.7384 (p)
REVERT: A  184 GLN cc_start: 0.7756 (mp10) cc_final: 0.7515 (mp10)
REVERT: A  254 ILE cc_start: 0.7211 (tp) cc_final: 0.6845 (tp)
REVERT: A  282 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7307 (mp)
REVERT: A  378 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.7031 (p)
REVERT: A  402 PHE cc_start: 0.6327 (t80) cc_final: 0.6126 (t80)
REVERT: A  405 SER cc_start: 0.8446 (p) cc_final: 0.8171 (m)
REVERT: A  409 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7719 (p)
REVERT: A  427 LYS cc_start: 0.7279 (tmtt) cc_final: 0.6808 (tttp)
REVERT: A  432 GLN cc_start: 0.8828 (mt0) cc_final: 0.8569 (mm-40)
REVERT: A  514 TRP cc_start: 0.6388 (m-10) cc_final: 0.5865 (m-10)
REVERT: A  547 ASN cc_start: 0.6690 (t0) cc_final: 0.6426 (t0)
REVERT: A  556 GLU cc_start: 0.6903 (tp30) cc_final: 0.6512 (tp30)
REVERT: A  574 ASN cc_start: 0.8033 (t0) cc_final: 0.7700 (t0)
REVERT: A  696 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.5140 (pt)
REVERT: A  715 LYS cc_start: 0.8876 (tttt) cc_final: 0.8449 (tptt)
REVERT: A  768 ASP cc_start: 0.6350 (p0) cc_final: 0.6145 (p0)
REVERT: B   86 MET cc_start: 0.7092 (mmm) cc_final: 0.6277 (mmm)
REVERT: C   45 ARG cc_start: 0.6713 (mtm-85) cc_final: 0.6205 (mtt180)
REVERT: C   80 LEU cc_start: 0.8660 (tp) cc_final: 0.8167 (tp)
REVERT: C  114 THR cc_start: 0.8344 (m) cc_final: 0.8072 (p)
  outliers start: 43
  outliers final: 24
  residues processed: 223
  average time/residue: 0.1851
  time to fit residues: 56.2659
Evaluate side-chains
  219 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  872 ILE
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 67 optimal weight:    0.3980
   chunk 21 optimal weight:    0.3980
   chunk 22 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 819 HIS
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.109802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.095277 restraints weight = 16292.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.097303 restraints weight = 10465.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.098749 restraints weight = 7534.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   7733  Z= 0.197
  Angle     :  0.702   8.110  10558  Z= 0.358
  Chirality :  0.046   0.270   1271
  Planarity :  0.005   0.055   1346
  Dihedral  :  8.052 114.625   1094
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  : 10.80 %
    Favored  : 88.80 %
  Rotamer:
    Outliers :  6.53 %
    Allowed  : 23.50 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.71 (0.25), residues: 1009
  helix: -1.23 (0.34), residues: 245
  sheet: -1.03 (0.33), residues: 238
  loop : -2.49 (0.25), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  53 
 HIS   0.007   0.001   HIS A 523 
 PHE   0.019   0.002   PHE A 410 
 TYR   0.011   0.002   TYR C  94 
 ARG   0.007   0.001   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04379 (  233)
  hydrogen bonds       : angle       5.36220 (  597)
  SS BOND              : bond        0.00532 (    2)
  SS BOND              : angle       1.57433 (    4)
  covalent geometry    : bond        0.00464 ( 7731)
  covalent geometry    : angle       0.70156 (10554)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 201
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ASP cc_start: 0.6206 (p0) cc_final: 0.5323 (p0)
REVERT: A   38 ARG cc_start: 0.6887 (mpt-90) cc_final: 0.6590 (mmt90)
REVERT: A   74 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8199 (mm-40)
REVERT: A   85 ASN cc_start: 0.7918 (p0) cc_final: 0.7703 (p0)
REVERT: A   86 SER cc_start: 0.8071 (p) cc_final: 0.7477 (p)
REVERT: A  254 ILE cc_start: 0.7275 (tp) cc_final: 0.6924 (tp)
REVERT: A  282 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7311 (mp)
REVERT: A  316 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7773 (mm-40)
REVERT: A  338 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7457 (mm110)
REVERT: A  378 VAL cc_start: 0.7701 (OUTLIER) cc_final: 0.7246 (p)
REVERT: A  402 PHE cc_start: 0.6285 (t80) cc_final: 0.6074 (t80)
REVERT: A  405 SER cc_start: 0.8479 (p) cc_final: 0.8192 (m)
REVERT: A  427 LYS cc_start: 0.7340 (tmtt) cc_final: 0.6767 (tptp)
REVERT: A  432 GLN cc_start: 0.8753 (mt0) cc_final: 0.8517 (mm-40)
REVERT: A  547 ASN cc_start: 0.7254 (t0) cc_final: 0.7046 (t0)
REVERT: A  556 GLU cc_start: 0.6984 (tp30) cc_final: 0.6550 (tp30)
REVERT: A  574 ASN cc_start: 0.8060 (t0) cc_final: 0.7648 (t0)
REVERT: A  696 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5223 (pt)
REVERT: A  715 LYS cc_start: 0.8770 (tttt) cc_final: 0.8438 (tptt)
REVERT: B   51 ILE cc_start: 0.7523 (mm) cc_final: 0.7268 (mm)
REVERT: B   86 MET cc_start: 0.7073 (mmm) cc_final: 0.6165 (mmm)
REVERT: C   80 LEU cc_start: 0.8512 (tp) cc_final: 0.7978 (tp)
REVERT: C   86 LYS cc_start: 0.8362 (mtmm) cc_final: 0.7954 (mttp)
REVERT: C  114 THR cc_start: 0.8298 (m) cc_final: 0.8076 (p)
  outliers start: 50
  outliers final: 39
  residues processed: 229
  average time/residue: 0.1746
  time to fit residues: 55.0312
Evaluate side-chains
  236 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 193
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   74 GLN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  753 GLN
Chi-restraints excluded: chain A residue  758 ASP
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9980
   chunk 55 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 819 HIS
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.109439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.095119 restraints weight = 16319.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.097110 restraints weight = 10487.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.098540 restraints weight = 7603.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.3848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7733  Z= 0.188
  Angle     :  0.693  10.804  10558  Z= 0.353
  Chirality :  0.045   0.277   1271
  Planarity :  0.005   0.055   1346
  Dihedral  :  8.124 116.042   1094
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  : 10.21 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 25.07 %
    Favored  : 68.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.25), residues: 1009
  helix: -1.35 (0.33), residues: 254
  sheet: -0.97 (0.34), residues: 237
  loop : -2.46 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  53 
 HIS   0.005   0.001   HIS A 526 
 PHE   0.016   0.002   PHE A 410 
 TYR   0.013   0.002   TYR B  60 
 ARG   0.005   0.001   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04278 (  233)
  hydrogen bonds       : angle       5.36362 (  597)
  SS BOND              : bond        0.00475 (    2)
  SS BOND              : angle       1.66558 (    4)
  covalent geometry    : bond        0.00444 ( 7731)
  covalent geometry    : angle       0.69197 (10554)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 191
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ARG cc_start: 0.7686 (ptp90) cc_final: 0.7321 (ptt180)
REVERT: A   85 ASN cc_start: 0.7845 (p0) cc_final: 0.7309 (p0)
REVERT: A   86 SER cc_start: 0.8073 (p) cc_final: 0.7411 (p)
REVERT: A  165 ASP cc_start: 0.7144 (t0) cc_final: 0.6879 (t0)
REVERT: A  184 GLN cc_start: 0.7627 (mp10) cc_final: 0.7299 (mp10)
REVERT: A  254 ILE cc_start: 0.7308 (tp) cc_final: 0.6941 (tp)
REVERT: A  316 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7728 (mm-40)
REVERT: A  338 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7357 (mm110)
REVERT: A  378 VAL cc_start: 0.7854 (OUTLIER) cc_final: 0.7398 (p)
REVERT: A  427 LYS cc_start: 0.7323 (tmtt) cc_final: 0.7017 (tptp)
REVERT: A  556 GLU cc_start: 0.7008 (tp30) cc_final: 0.6572 (tp30)
REVERT: A  574 ASN cc_start: 0.8107 (t0) cc_final: 0.7659 (t0)
REVERT: A  715 LYS cc_start: 0.8770 (tttt) cc_final: 0.8408 (tptt)
REVERT: B   51 ILE cc_start: 0.7497 (mm) cc_final: 0.7138 (mt)
REVERT: B   86 MET cc_start: 0.6971 (mmm) cc_final: 0.6086 (mmm)
REVERT: C   80 LEU cc_start: 0.8538 (tp) cc_final: 0.7994 (tp)
REVERT: C   86 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7897 (mttp)
  outliers start: 47
  outliers final: 41
  residues processed: 217
  average time/residue: 0.1744
  time to fit residues: 51.5329
Evaluate side-chains
  225 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 183
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  753 GLN
Chi-restraints excluded: chain A residue  758 ASP
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0060
   chunk 1 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 19 optimal weight:    0.2980
   chunk 33 optimal weight:    0.8980
   chunk 17 optimal weight:    0.3980
   chunk 98 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A 819 HIS
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.110228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.095635 restraints weight = 16501.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.097754 restraints weight = 10624.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.099217 restraints weight = 7612.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7733  Z= 0.156
  Angle     :  0.666   7.745  10558  Z= 0.339
  Chirality :  0.045   0.266   1271
  Planarity :  0.005   0.055   1346
  Dihedral  :  7.970 117.756   1094
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  9.71 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 25.72 %
    Favored  : 67.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.26), residues: 1009
  helix: -1.32 (0.33), residues: 252
  sheet: -0.89 (0.34), residues: 237
  loop : -2.42 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  91 
 HIS   0.003   0.001   HIS A 526 
 PHE   0.015   0.002   PHE A 410 
 TYR   0.012   0.002   TYR C  94 
 ARG   0.005   0.001   ARG C  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  233)
  hydrogen bonds       : angle       5.27372 (  597)
  SS BOND              : bond        0.00410 (    2)
  SS BOND              : angle       1.36837 (    4)
  covalent geometry    : bond        0.00370 ( 7731)
  covalent geometry    : angle       0.66579 (10554)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 185
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ARG cc_start: 0.7721 (ptp90) cc_final: 0.7476 (ptt180)
REVERT: A   85 ASN cc_start: 0.7777 (p0) cc_final: 0.7538 (p0)
REVERT: A   86 SER cc_start: 0.7984 (p) cc_final: 0.7338 (p)
REVERT: A  165 ASP cc_start: 0.7147 (t0) cc_final: 0.6945 (t0)
REVERT: A  184 GLN cc_start: 0.7633 (mp10) cc_final: 0.7333 (mp10)
REVERT: A  254 ILE cc_start: 0.7252 (tp) cc_final: 0.6936 (tp)
REVERT: A  316 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7916 (mm-40)
REVERT: A  338 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7389 (mm110)
REVERT: A  378 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7492 (p)
REVERT: A  427 LYS cc_start: 0.7325 (tmtt) cc_final: 0.7059 (tptp)
REVERT: A  556 GLU cc_start: 0.6914 (tp30) cc_final: 0.6482 (tp30)
REVERT: A  715 LYS cc_start: 0.8759 (tttt) cc_final: 0.8411 (tptt)
REVERT: B   51 ILE cc_start: 0.7450 (mm) cc_final: 0.7066 (mt)
REVERT: B   86 MET cc_start: 0.7062 (mmm) cc_final: 0.6204 (mmm)
REVERT: C   80 LEU cc_start: 0.8393 (tp) cc_final: 0.7904 (tp)
  outliers start: 49
  outliers final: 37
  residues processed: 217
  average time/residue: 0.1809
  time to fit residues: 53.5557
Evaluate side-chains
  215 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 177
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  753 GLN
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 33 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 99 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 819 HIS
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.108700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.094411 restraints weight = 16402.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.096429 restraints weight = 10555.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.097840 restraints weight = 7626.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.4234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   7733  Z= 0.207
  Angle     :  0.723  10.596  10558  Z= 0.369
  Chirality :  0.046   0.229   1271
  Planarity :  0.005   0.057   1346
  Dihedral  :  8.205 122.704   1094
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  : 11.20 %
    Favored  : 88.40 %
  Rotamer:
    Outliers :  6.66 %
    Allowed  : 25.85 %
    Favored  : 67.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.25), residues: 1009
  helix: -1.39 (0.33), residues: 238
  sheet: -0.91 (0.34), residues: 237
  loop : -2.45 (0.25), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 333 
 HIS   0.004   0.001   HIS A 718 
 PHE   0.015   0.002   PHE A 115 
 TYR   0.013   0.002   TYR A 767 
 ARG   0.005   0.001   ARG C  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04359 (  233)
  hydrogen bonds       : angle       5.52173 (  597)
  SS BOND              : bond        0.00545 (    2)
  SS BOND              : angle       1.65476 (    4)
  covalent geometry    : bond        0.00488 ( 7731)
  covalent geometry    : angle       0.72266 (10554)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 185
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ARG cc_start: 0.7772 (ptp90) cc_final: 0.7435 (ptt180)
REVERT: A   86 SER cc_start: 0.7993 (p) cc_final: 0.7540 (p)
REVERT: A  184 GLN cc_start: 0.7669 (mp10) cc_final: 0.7402 (mp10)
REVERT: A  254 ILE cc_start: 0.7238 (tp) cc_final: 0.6953 (tp)
REVERT: A  338 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7525 (mm110)
REVERT: A  378 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7750 (m)
REVERT: A  427 LYS cc_start: 0.7375 (tmtt) cc_final: 0.7163 (tptp)
REVERT: A  556 GLU cc_start: 0.6704 (tp30) cc_final: 0.6271 (tp30)
REVERT: A  574 ASN cc_start: 0.7834 (t0) cc_final: 0.7494 (t0)
REVERT: A  715 LYS cc_start: 0.8726 (tttt) cc_final: 0.8381 (tptt)
REVERT: B   51 ILE cc_start: 0.7464 (mm) cc_final: 0.7122 (mt)
REVERT: B   86 MET cc_start: 0.7059 (mmm) cc_final: 0.6212 (mmm)
REVERT: C   80 LEU cc_start: 0.8602 (tp) cc_final: 0.8097 (tp)
  outliers start: 51
  outliers final: 42
  residues processed: 213
  average time/residue: 0.1674
  time to fit residues: 49.5893
Evaluate side-chains
  222 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 179
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  753 GLN
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 81 optimal weight:    7.9990
   chunk 51 optimal weight:    0.3980
   chunk 88 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    0.1980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 819 HIS
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.110162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.095725 restraints weight = 16450.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.097784 restraints weight = 10424.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.099257 restraints weight = 7450.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7733  Z= 0.155
  Angle     :  0.681   9.056  10558  Z= 0.347
  Chirality :  0.045   0.187   1271
  Planarity :  0.005   0.058   1346
  Dihedral  :  7.937 124.328   1094
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  9.22 %
    Favored  : 90.39 %
  Rotamer:
    Outliers :  6.66 %
    Allowed  : 27.42 %
    Favored  : 65.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.25), residues: 1009
  helix: -1.33 (0.33), residues: 244
  sheet: -0.90 (0.34), residues: 237
  loop : -2.38 (0.25), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  53 
 HIS   0.005   0.001   HIS A 526 
 PHE   0.015   0.002   PHE A 115 
 TYR   0.016   0.002   TYR A 684 
 ARG   0.006   0.001   ARG C  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03919 (  233)
  hydrogen bonds       : angle       5.31103 (  597)
  SS BOND              : bond        0.00402 (    2)
  SS BOND              : angle       1.37583 (    4)
  covalent geometry    : bond        0.00366 ( 7731)
  covalent geometry    : angle       0.68073 (10554)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 186
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ASP cc_start: 0.6286 (p0) cc_final: 0.5386 (p0)
REVERT: A   54 ARG cc_start: 0.7757 (ptp90) cc_final: 0.7435 (ptt180)
REVERT: A   74 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8096 (mt0)
REVERT: A   86 SER cc_start: 0.7961 (p) cc_final: 0.7345 (p)
REVERT: A  254 ILE cc_start: 0.7310 (tp) cc_final: 0.7013 (tp)
REVERT: A  338 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7545 (mm110)
REVERT: A  378 VAL cc_start: 0.7972 (OUTLIER) cc_final: 0.7701 (m)
REVERT: A  427 LYS cc_start: 0.7283 (tmtt) cc_final: 0.6709 (tptp)
REVERT: A  556 GLU cc_start: 0.6585 (tp30) cc_final: 0.6187 (tp30)
REVERT: A  574 ASN cc_start: 0.7884 (t0) cc_final: 0.7513 (t0)
REVERT: A  715 LYS cc_start: 0.8721 (tttt) cc_final: 0.8366 (tptt)
REVERT: B   51 ILE cc_start: 0.7474 (mm) cc_final: 0.7095 (mt)
REVERT: B   86 MET cc_start: 0.7083 (mmm) cc_final: 0.6240 (mmm)
REVERT: C   80 LEU cc_start: 0.8551 (tp) cc_final: 0.8029 (tp)
  outliers start: 51
  outliers final: 42
  residues processed: 216
  average time/residue: 0.1712
  time to fit residues: 50.7126
Evaluate side-chains
  225 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 181
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   74 GLN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  365 SER
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  434 PHE
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  716 ASN
Chi-restraints excluded: chain A residue  753 GLN
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0770
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A 184 GLN
** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 718 HIS
A 819 HIS
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.109587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.095335 restraints weight = 16503.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.097371 restraints weight = 10486.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.098766 restraints weight = 7505.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.4428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7733  Z= 0.185
  Angle     :  0.703   8.071  10558  Z= 0.357
  Chirality :  0.045   0.189   1271
  Planarity :  0.005   0.058   1346
  Dihedral  :  8.101 126.775   1094
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 10.41 %
    Favored  : 89.30 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 28.46 %
    Favored  : 65.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.25), residues: 1009
  helix: -1.21 (0.34), residues: 232
  sheet: -1.01 (0.34), residues: 237
  loop : -2.38 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  53 
 HIS   0.005   0.001   HIS A 526 
 PHE   0.015   0.002   PHE A 115 
 TYR   0.038   0.002   TYR A 767 
 ARG   0.007   0.001   ARG C  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04075 (  233)
  hydrogen bonds       : angle       5.46947 (  597)
  SS BOND              : bond        0.00480 (    2)
  SS BOND              : angle       1.57937 (    4)
  covalent geometry    : bond        0.00438 ( 7731)
  covalent geometry    : angle       0.70287 (10554)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 188
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ASP cc_start: 0.6068 (p0) cc_final: 0.5699 (p0)
REVERT: A   38 ARG cc_start: 0.6625 (mmt90) cc_final: 0.6355 (mmt90)
REVERT: A   54 ARG cc_start: 0.7783 (ptp90) cc_final: 0.7450 (ptt180)
REVERT: A   74 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8081 (mt0)
REVERT: A   86 SER cc_start: 0.7921 (p) cc_final: 0.7312 (p)
REVERT: A  254 ILE cc_start: 0.7215 (tp) cc_final: 0.6961 (tp)
REVERT: A  338 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7573 (mm110)
REVERT: A  378 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7733 (m)
REVERT: A  547 ASN cc_start: 0.7355 (t0) cc_final: 0.7091 (p0)
REVERT: A  556 GLU cc_start: 0.6579 (tp30) cc_final: 0.6180 (tp30)
REVERT: A  574 ASN cc_start: 0.7879 (t0) cc_final: 0.7502 (t0)
REVERT: A  715 LYS cc_start: 0.8694 (tttt) cc_final: 0.8368 (tptt)
REVERT: B   51 ILE cc_start: 0.7451 (mm) cc_final: 0.7098 (mt)
REVERT: B   86 MET cc_start: 0.7052 (mmm) cc_final: 0.6161 (mmm)
REVERT: C   80 LEU cc_start: 0.8549 (tp) cc_final: 0.8012 (tp)
  outliers start: 43
  outliers final: 40
  residues processed: 214
  average time/residue: 0.1668
  time to fit residues: 49.7112
Evaluate side-chains
  229 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 187
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   74 GLN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   93 ASP
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  177 GLU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  716 ASN
Chi-restraints excluded: chain A residue  753 GLN
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    0.0870
   chunk 46 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0670
   chunk 43 optimal weight:    0.5980
   chunk 83 optimal weight:    1.9990
   chunk 64 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.3496

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

Flipped N/Q/H residues before XYZ refinement:
A 184 GLN
** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 819 HIS
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.111041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.096546 restraints weight = 16518.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.098631 restraints weight = 10508.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.100094 restraints weight = 7525.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.4451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7733  Z= 0.139
  Angle     :  0.700   8.982  10558  Z= 0.355
  Chirality :  0.044   0.183   1271
  Planarity :  0.005   0.057   1346
  Dihedral  :  7.812 128.084   1094
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.12 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 29.37 %
    Favored  : 65.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.26), residues: 1009
  helix: -1.19 (0.34), residues: 238
  sheet: -0.99 (0.34), residues: 238
  loop : -2.29 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  53 
 HIS   0.004   0.001   HIS A 526 
 PHE   0.016   0.002   PHE A 410 
 TYR   0.025   0.002   TYR A 767 
 ARG   0.008   0.000   ARG C  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03769 (  233)
  hydrogen bonds       : angle       5.31927 (  597)
  SS BOND              : bond        0.00311 (    2)
  SS BOND              : angle       1.21099 (    4)
  covalent geometry    : bond        0.00327 ( 7731)
  covalent geometry    : angle       0.69928 (10554)

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

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

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2018 Ramachandran restraints generated.
    1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 187
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ARG cc_start: 0.7771 (ptp90) cc_final: 0.7444 (ptt180)
REVERT: A   74 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8096 (mt0)
REVERT: A   86 SER cc_start: 0.7872 (p) cc_final: 0.7205 (p)
REVERT: A  254 ILE cc_start: 0.7320 (tp) cc_final: 0.7050 (tp)
REVERT: A  338 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7579 (mm110)
REVERT: A  378 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7676 (m)
REVERT: A  380 ARG cc_start: 0.7065 (mpt180) cc_final: 0.6756 (mmt90)
REVERT: A  427 LYS cc_start: 0.7309 (tptp) cc_final: 0.7084 (tptp)
REVERT: A  432 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8310 (mm-40)
REVERT: A  514 TRP cc_start: 0.6364 (m-10) cc_final: 0.6147 (m-10)
REVERT: A  547 ASN cc_start: 0.7328 (t0) cc_final: 0.7058 (p0)
REVERT: A  556 GLU cc_start: 0.6621 (tp30) cc_final: 0.6261 (tp30)
REVERT: A  574 ASN cc_start: 0.7872 (t0) cc_final: 0.7490 (t0)
REVERT: A  715 LYS cc_start: 0.8718 (tttt) cc_final: 0.8348 (tptt)
REVERT: B   51 ILE cc_start: 0.7481 (mm) cc_final: 0.7090 (mt)
REVERT: B   86 MET cc_start: 0.7072 (mmm) cc_final: 0.6175 (mmm)
REVERT: C   80 LEU cc_start: 0.8544 (tp) cc_final: 0.8036 (tp)
  outliers start: 39
  outliers final: 35
  residues processed: 213
  average time/residue: 0.1675
  time to fit residues: 49.5351
Evaluate side-chains
  222 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 185
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ILE
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   74 GLN
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  325 SER
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  618 LEU
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  716 ASN
Chi-restraints excluded: chain A residue  753 GLN
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   57 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    0.0870
   chunk 97 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0050
   chunk 3 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0980
   chunk 23 optimal weight:    0.0470
   chunk 52 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.1670

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

Flipped N/Q/H residues before XYZ refinement:
A 184 GLN
** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.113896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.099358 restraints weight = 16300.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.101507 restraints weight = 10317.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.103050 restraints weight = 7339.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
moved from start:          0.4580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7733  Z= 0.118
  Angle     :  0.669   8.779  10558  Z= 0.337
  Chirality :  0.044   0.177   1271
  Planarity :  0.005   0.055   1346
  Dihedral  :  7.365 126.714   1093
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.72 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 29.77 %
    Favored  : 65.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.26), residues: 1009
  helix: -0.97 (0.35), residues: 236
  sheet: -0.99 (0.33), residues: 236
  loop : -2.18 (0.25), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 827 
 HIS   0.004   0.001   HIS A 526 
 PHE   0.017   0.002   PHE A 410 
 TYR   0.019   0.001   TYR A 767 
 ARG   0.008   0.001   ARG C  66 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03378 (  233)
  hydrogen bonds       : angle       5.06668 (  597)
  SS BOND              : bond        0.00153 (    2)
  SS BOND              : angle       0.91709 (    4)
  covalent geometry    : bond        0.00274 ( 7731)
  covalent geometry    : angle       0.66893 (10554)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2580.44 seconds
wall clock time: 45 minutes 51.94 seconds (2751.94 seconds total)