Starting phenix.real_space_refine
on Sun Jun 15 18:36:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d3u_27164/06_2025/8d3u_27164_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d3u_27164/06_2025/8d3u_27164.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d3u_27164/06_2025/8d3u_27164.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d3u_27164/06_2025/8d3u_27164.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d3u_27164/06_2025/8d3u_27164_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d3u_27164/06_2025/8d3u_27164_neut.cif"
  }
  resolution = 3.7
  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=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9272 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       2      5.49       5
     S      60      5.16       5
     C    6462      2.51       5
     N    1689      2.21       5
     O    1903      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10121
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 971, 7521
          Classifications: {'peptide': 971}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 41, 'TRANS': 929}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2322
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2322
          Classifications: {'peptide': 285}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 264}
    Chain: "G"
      Number of atoms: 246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 246
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 1, 'TRANS': 29}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {'ADP': 1, 'ALF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.54, per 1000 atoms: 0.65
  Number of scatterers: 10121
  At special positions: 0
  Unit cell: (143.59, 98.77, 131.14, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      60     16.00
     P       2     15.00
     Al      1     13.00
     F       4      9.00
     O    1903      8.00
     N    1689      7.00
     C    6462      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  42 " - pdb=" SG  CYS A  49 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 126 " - pdb=" SG  CYS B 149 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 213 " - pdb=" SG  CYS B 276 " 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: 2.49
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2376

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 9 sheets defined
      47.9% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 45
      removed outlier: 3.824A  pdb=" N   TYR A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 66
      removed outlier: 3.541A  pdb=" N   GLN A  59 " --> pdb=" O   HIS A  55 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLU A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 88
      removed outlier: 3.720A  pdb=" N   CYS A  83 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 110
    Processing helix  chain 'A' and resid 119 through 153
      removed outlier: 3.587A  pdb=" N   ILE A 147 " --> pdb=" O   LYS A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 260
      removed outlier: 3.873A  pdb=" N   ILE A 260 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 304
    Processing helix  chain 'A' and resid 306 through 321
    Processing helix  chain 'A' and resid 325 through 343
    Processing helix  chain 'A' and resid 352 through 359
      removed outlier: 3.927A  pdb=" N   THR A 356 " --> pdb=" O   GLU A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 419
      removed outlier: 3.774A  pdb=" N   ASN A 419 " --> pdb=" O   ALA A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 454
    Processing helix  chain 'A' and resid 456 through 464
    Processing helix  chain 'A' and resid 500 through 507
    Processing helix  chain 'A' and resid 521 through 538
      removed outlier: 3.716A  pdb=" N   LEU A 538 " --> pdb=" O   GLU A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 610 through 622
    Processing helix  chain 'A' and resid 630 through 639
    Processing helix  chain 'A' and resid 641 through 645
    Processing helix  chain 'A' and resid 658 through 662
    Processing helix  chain 'A' and resid 664 through 675
    Processing helix  chain 'A' and resid 684 through 697
    Processing helix  chain 'A' and resid 708 through 710
      No H-bonds generated for 'chain 'A' and resid 708 through 710'
    Processing helix  chain 'A' and resid 711 through 718
    Processing helix  chain 'A' and resid 729 through 736
    Processing helix  chain 'A' and resid 746 through 770
      removed outlier: 3.585A  pdb=" N   THR A 750 " --> pdb=" O   ALA A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 787
      Proline residue:  A 779  - end of helix
    Processing helix  chain 'A' and resid 793 through 805
    Processing helix  chain 'A' and resid 806 through 812
      removed outlier: 3.652A  pdb=" N   ILE A 810 " --> pdb=" O   MET A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 815
      No H-bonds generated for 'chain 'A' and resid 813 through 815'
    Processing helix  chain 'A' and resid 836 through 845
    Processing helix  chain 'A' and resid 847 through 867
    Processing helix  chain 'A' and resid 869 through 873
      removed outlier: 3.581A  pdb=" N   LEU A 873 " --> pdb=" O   PRO A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 881
    Processing helix  chain 'A' and resid 897 through 927
      removed outlier: 3.804A  pdb=" N   ALA A 922 " --> pdb=" O   VAL A 918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 933 through 938
    Processing helix  chain 'A' and resid 941 through 961
      removed outlier: 3.761A  pdb=" N   ILE A 945 " --> pdb=" O   ASN A 941 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   SER A 959 " --> pdb=" O   ALA A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 963 through 968
      removed outlier: 3.872A  pdb=" N   ALA A 967 " --> pdb=" O   GLY A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 980
      removed outlier: 3.852A  pdb=" N   PHE A 979 " --> pdb=" O   SER A 976 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   CYS A 980 " --> pdb=" O   TRP A 977 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 1002
    Processing helix  chain 'A' and resid 1005 through 1011
    Processing helix  chain 'B' and resid 34 through 61
      removed outlier: 3.633A  pdb=" N   THR B  60 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 73
      removed outlier: 3.509A  pdb=" N   ALA B  73 " --> pdb=" O   ASP B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 97
    Processing helix  chain 'B' and resid 98 through 110
      removed outlier: 3.825A  pdb=" N   ASN B 104 " --> pdb=" O   ALA B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 113
      No H-bonds generated for 'chain 'B' and resid 111 through 113'
    Processing helix  chain 'B' and resid 152 through 157
    Processing helix  chain 'B' and resid 217 through 222
      removed outlier: 3.719A  pdb=" N   ASP B 222 " --> pdb=" O   ASP B 218 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 36 through 58
      removed outlier: 4.082A  pdb=" N   ILE G  56 " --> pdb=" O   GLY G  52 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   LEU G  57 " --> pdb=" O   ILE G  53 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171
      removed outlier: 3.902A  pdb=" N   VAL A 161 " --> pdb=" O   MET A 168 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   LEU A 160 " --> pdb=" O   GLU A 182 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LEU A 180 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   CYS A 239 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   VAL A 203 " --> pdb=" O   CYS A 239 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   GLU A 241 " --> pdb=" O   CYS A 201 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   CYS A 201 " --> pdb=" O   GLU A 241 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   VAL A 247 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   ILE A 195 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188
      removed outlier: 3.561A  pdb=" N   ASP A 187 " --> pdb=" O   CYS A 239 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   CYS A 239 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   VAL A 203 " --> pdb=" O   CYS A 239 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   GLU A 241 " --> pdb=" O   CYS A 201 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   CYS A 201 " --> pdb=" O   GLU A 241 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   VAL A 247 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   ILE A 195 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 348
      removed outlier: 6.762A  pdb=" N   VAL A 702 " --> pdb=" O   ILE A 720 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   VAL A 722 " --> pdb=" O   VAL A 702 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   VAL A 704 " --> pdb=" O   VAL A 722 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   MET A 724 " --> pdb=" O   VAL A 704 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   GLY A 706 " --> pdb=" O   MET A 724 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   ILE A 363 " --> pdb=" O   ILE A 604 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 389
      removed outlier: 3.685A  pdb=" N   THR A 377 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   SER A 580 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   MET A 381 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LEU A 578 " --> pdb=" O   MET A 381 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   PHE A 545 " --> pdb=" O   VAL A 576 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   LEU A 578 " --> pdb=" O   LEU A 543 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LEU A 543 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   SER A 580 " --> pdb=" O   ARG A 541 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ARG A 541 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   LEU A 480 " --> pdb=" O   GLU A 469 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   GLU A 469 " --> pdb=" O   LEU A 480 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ILE A 482 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 387 through 389
      removed outlier: 3.685A  pdb=" N   THR A 377 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   SER A 580 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   MET A 381 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LEU A 578 " --> pdb=" O   MET A 381 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   CYS A 508 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   PHE A 575 " --> pdb=" O   CYS A 508 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   THR A 510 " --> pdb=" O   PHE A 575 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   GLY A 577 " --> pdb=" O   THR A 510 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 422 through 423
    Processing sheet with id=AA7, first strand: chain 'A' and resid 652 through 653
    Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 79
      removed outlier: 3.727A  pdb=" N   ALA B 260 " --> pdb=" O   PHE B 230 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90
      removed outlier: 3.618A  pdb=" N   PHE B  90 " --> pdb=" O   GLU B 300 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1386 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: 3.63

  Time building geometry restraints manager: 3.00 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3303
        1.35 -     1.46: 2297
        1.46 -     1.58: 4634
        1.58 -     1.70: 5
        1.70 -     1.82: 92
  Bond restraints: 10331
  Sorted by residual:
  bond pdb=" C3' ADP A1101 "
       pdb=" C4' ADP A1101 "
    ideal  model  delta    sigma   weight residual
    1.524  1.305  0.219 2.00e-02 2.50e+03 1.20e+02
  bond pdb=" C4' ADP A1101 "
       pdb=" O4' ADP A1101 "
    ideal  model  delta    sigma   weight residual
    1.426  1.614 -0.188 2.00e-02 2.50e+03 8.83e+01
  bond pdb=" C4  ADP A1101 "
       pdb=" C5  ADP A1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.334  0.156 2.00e-02 2.50e+03 6.05e+01
  bond pdb=" F2  ALF A1102 "
       pdb="AL   ALF A1102 "
    ideal  model  delta    sigma   weight residual
    1.685  1.808 -0.123 2.00e-02 2.50e+03 3.78e+01
  bond pdb=" C1' ADP A1101 "
       pdb=" O4' ADP A1101 "
    ideal  model  delta    sigma   weight residual
    1.426  1.305  0.121 2.00e-02 2.50e+03 3.64e+01
  ... (remaining 10326 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.99: 13996
       13.99 -    27.98: 7
       27.98 -    41.97: 0
       41.97 -    55.96: 0
       55.96 -    69.95: 2
  Bond angle restraints: 14005
  Sorted by residual:
  angle pdb=" F3  ALF A1102 "
        pdb="AL   ALF A1102 "
        pdb=" F4  ALF A1102 "
      ideal   model   delta    sigma   weight residual
     109.63  179.58  -69.95 3.00e+00 1.11e-01 5.44e+02
  angle pdb=" F1  ALF A1102 "
        pdb="AL   ALF A1102 "
        pdb=" F2  ALF A1102 "
      ideal   model   delta    sigma   weight residual
     108.68  178.40  -69.72 3.00e+00 1.11e-01 5.40e+02
  angle pdb=" N   GLU A  33 "
        pdb=" CA  GLU A  33 "
        pdb=" CB  GLU A  33 "
      ideal   model   delta    sigma   weight residual
     110.50  130.21  -19.71 1.70e+00 3.46e-01 1.34e+02
  angle pdb=" C1' ADP A1101 "
        pdb=" N9  ADP A1101 "
        pdb=" C8  ADP A1101 "
      ideal   model   delta    sigma   weight residual
     126.00  104.64   21.36 3.00e+00 1.11e-01 5.07e+01
  angle pdb=" F2  ALF A1102 "
        pdb="AL   ALF A1102 "
        pdb=" F4  ALF A1102 "
      ideal   model   delta    sigma   weight residual
     110.21   89.68   20.53 3.00e+00 1.11e-01 4.68e+01
  ... (remaining 14000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.31: 5909
       31.31 -    62.61: 277
       62.61 -    93.92: 27
       93.92 -   125.22: 0
      125.22 -   156.53: 2
  Dihedral angle restraints: 6215
    sinusoidal: 2513
      harmonic: 3702
  Sorted by residual:
  dihedral pdb=" N   GLU A  33 "
           pdb=" C   GLU A  33 "
           pdb=" CA  GLU A  33 "
           pdb=" CB  GLU A  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  151.63  -28.83     0      2.50e+00 1.60e-01 1.33e+02
  dihedral pdb=" CB  CYS A  42 "
           pdb=" SG  CYS A  42 "
           pdb=" SG  CYS A  49 "
           pdb=" CB  CYS A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    6.73   86.27     1      1.00e+01 1.00e-02 8.98e+01
  dihedral pdb=" C   GLU A  33 "
           pdb=" N   GLU A  33 "
           pdb=" CA  GLU A  33 "
           pdb=" CB  GLU A  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -144.64   22.04     0      2.50e+00 1.60e-01 7.77e+01
  ... (remaining 6212 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.219: 1577
       0.219 -    0.439: 1
       0.439 -    0.658: 0
       0.658 -    0.877: 0
       0.877 -    1.097: 1
  Chirality restraints: 1579
  Sorted by residual:
  chirality pdb=" CA  GLU A  33 "
            pdb=" N   GLU A  33 "
            pdb=" C   GLU A  33 "
            pdb=" CB  GLU A  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.41    1.10 2.00e-01 2.50e+01 3.01e+01
  chirality pdb=" CB  ILE A 926 "
            pdb=" CA  ILE A 926 "
            pdb=" CG1 ILE A 926 "
            pdb=" CG2 ILE A 926 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  MET B 121 "
            pdb=" N   MET B 121 "
            pdb=" C   MET B 121 "
            pdb=" CB  MET B 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 1576 not shown)

  Planarity restraints: 1804
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  66 "   -0.043 5.00e-02 4.00e+02   6.37e-02 6.49e+00
        pdb=" N   PRO A  67 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A  67 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  67 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 120 "    0.011 2.00e-02 2.50e+03   2.27e-02 5.14e+00
        pdb=" C   ASP B 120 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ASP B 120 "    0.015 2.00e-02 2.50e+03
        pdb=" N   MET B 121 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 610 "    0.032 5.00e-02 4.00e+02   4.89e-02 3.82e+00
        pdb=" N   PRO A 611 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 611 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 611 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1801 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.09: 2
        2.09 -     2.79: 2662
        2.79 -     3.50: 14548
        3.50 -     4.20: 23013
        4.20 -     4.90: 41948
  Nonbonded interactions: 82173
  Sorted by model distance:
  nonbonded pdb=" O   TYR G  34 "
            pdb=" N   THR G  36 "
     model   vdw
     1.392 3.120
  nonbonded pdb=" O   TYR G  34 "
            pdb=" N   LEU G  37 "
     model   vdw
     2.087 3.120
  nonbonded pdb=" O2B ADP A1101 "
            pdb=" F2  ALF A1102 "
     model   vdw
     2.149 2.990
  nonbonded pdb=" O   THR A 368 "
            pdb=" F3  ALF A1102 "
     model   vdw
     2.162 2.990
  nonbonded pdb=" N   ASP G  33 "
            pdb=" OD1 ASP G  33 "
     model   vdw
     2.174 3.120
  ... (remaining 82168 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.120
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.870
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.219  10334  Z= 0.262
  Angle     :  1.154  69.952  14011  Z= 0.482
  Chirality :  0.050   1.097   1579
  Planarity :  0.004   0.064   1804
  Dihedral  : 17.659 156.527   3830
  Min Nonbonded Distance : 1.392

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.24 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 27.89 %
    Favored  : 71.48 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    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:  0.50 (0.24), residues: 1279
  helix:  1.81 (0.23), residues: 539
  sheet: -0.31 (0.51), residues: 121
  loop : -0.88 (0.26), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  79 
 HIS   0.002   0.001   HIS A 656 
 PHE   0.017   0.001   PHE G  44 
 TYR   0.014   0.001   TYR A 859 
 ARG   0.002   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14141 (  474)
  hydrogen bonds       : angle       5.99455 ( 1386)
  SS BOND              : bond        0.00372 (    3)
  SS BOND              : angle       1.27648 (    6)
  covalent geometry    : bond        0.00533 (10331)
  covalent geometry    : angle       1.15427 (14005)

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

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

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 130
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   33 ASP cc_start: 0.2422 (OUTLIER) cc_final: 0.2052 (p0)
  outliers start: 7
  outliers final: 3
  residues processed: 136
  average time/residue: 0.1859
  time to fit residues: 38.1614
Evaluate side-chains
  132 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  887 ASP
Chi-restraints excluded: chain G residue   33 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    0.0050
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.1980
   chunk 74 optimal weight:    0.9990
   chunk 116 optimal weight:    3.9990
   overall best weight:    0.9998

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
A 223 HIS
A 283 GLN
A 479 GLN
A 530 ASN
A 554 GLN
A 866 ASN
A 920 GLN
A 936 GLN
B 234 ASN
B 265 ASN
G  31 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.106930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.085778 restraints weight = 22568.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.088333 restraints weight = 12276.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.089912 restraints weight = 8194.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.0832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10334  Z= 0.127
  Angle     :  0.594   9.704  14011  Z= 0.301
  Chirality :  0.042   0.169   1579
  Planarity :  0.004   0.046   1804
  Dihedral  :  6.276 109.974   1404
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.85 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 25.54 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.57 (0.25), residues: 1279
  helix:  1.84 (0.23), residues: 557
  sheet: -0.53 (0.47), residues: 141
  loop : -0.83 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  79 
 HIS   0.003   0.001   HIS G  31 
 PHE   0.017   0.001   PHE A 783 
 TYR   0.013   0.001   TYR A 859 
 ARG   0.003   0.000   ARG A 877 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03481 (  474)
  hydrogen bonds       : angle       4.36943 ( 1386)
  SS BOND              : bond        0.00855 (    3)
  SS BOND              : angle       2.08096 (    6)
  covalent geometry    : bond        0.00292 (10331)
  covalent geometry    : angle       0.59228 (14005)

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

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

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 147
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 CYS cc_start: 0.8113 (m) cc_final: 0.7392 (t)
REVERT: A   90 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7381 (t80)
REVERT: A  466 LYS cc_start: 0.7641 (ttmt) cc_final: 0.7348 (tttt)
REVERT: A  568 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.5903 (m-80)
REVERT: G   35 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7951 (tm-30)
  outliers start: 30
  outliers final: 12
  residues processed: 166
  average time/residue: 0.1784
  time to fit residues: 45.7338
Evaluate side-chains
  146 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 PHE
Chi-restraints excluded: chain A residue  168 MET
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  568 PHE
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  754 GLU
Chi-restraints excluded: chain A residue  806 MET
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain G residue   53 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 121 optimal weight:    0.0570
   chunk 21 optimal weight:   20.0000
   chunk 59 optimal weight:    0.0020
   chunk 4 optimal weight:    8.9990
   chunk 70 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    2.4112

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 169 GLN
A 476 ASN
A 479 GLN
B 241 GLN
B 262 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.104918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.084472 restraints weight = 22790.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.087141 restraints weight = 12452.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.088620 restraints weight = 8089.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10334  Z= 0.189
  Angle     :  0.607   8.763  14011  Z= 0.310
  Chirality :  0.043   0.177   1579
  Planarity :  0.004   0.045   1804
  Dihedral  :  6.330 119.187   1396
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.47 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.81 %
    Favored  : 70.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.56 (0.24), residues: 1279
  helix:  1.79 (0.23), residues: 561
  sheet: -0.60 (0.47), residues: 136
  loop : -0.79 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  79 
 HIS   0.002   0.001   HIS A 656 
 PHE   0.020   0.001   PHE A 783 
 TYR   0.016   0.002   TYR A 859 
 ARG   0.005   0.000   ARG A 648 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03517 (  474)
  hydrogen bonds       : angle       4.24997 ( 1386)
  SS BOND              : bond        0.00382 (    3)
  SS BOND              : angle       1.39473 (    6)
  covalent geometry    : bond        0.00439 (10331)
  covalent geometry    : angle       0.60666 (14005)

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

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

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 135
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 CYS cc_start: 0.8154 (m) cc_final: 0.7497 (t)
REVERT: A  418 CYS cc_start: 0.8277 (t) cc_final: 0.7971 (t)
REVERT: A  466 LYS cc_start: 0.7645 (ttmt) cc_final: 0.7135 (mtpt)
REVERT: A  568 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6102 (m-80)
REVERT: A  901 ARG cc_start: 0.9092 (ptp90) cc_final: 0.8634 (ptt90)
REVERT: G   35 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7127 (tm-30)
  outliers start: 41
  outliers final: 20
  residues processed: 170
  average time/residue: 0.1710
  time to fit residues: 45.1969
Evaluate side-chains
  144 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  568 PHE
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  754 GLU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  917 VAL
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   53 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 115 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   chunk 20 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 118 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
G  31 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.106308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.085724 restraints weight = 22406.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.088314 restraints weight = 12112.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.089851 restraints weight = 8027.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10334  Z= 0.127
  Angle     :  0.571   8.208  14011  Z= 0.288
  Chirality :  0.042   0.152   1579
  Planarity :  0.004   0.046   1804
  Dihedral  :  6.207 119.923   1396
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.38 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 25.81 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.60 (0.24), residues: 1279
  helix:  1.87 (0.23), residues: 559
  sheet: -0.73 (0.46), residues: 145
  loop : -0.78 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  79 
 HIS   0.003   0.001   HIS G  31 
 PHE   0.022   0.001   PHE A 291 
 TYR   0.014   0.001   TYR A 859 
 ARG   0.004   0.000   ARG A 648 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03105 (  474)
  hydrogen bonds       : angle       4.05134 ( 1386)
  SS BOND              : bond        0.00307 (    3)
  SS BOND              : angle       1.34619 (    6)
  covalent geometry    : bond        0.00293 (10331)
  covalent geometry    : angle       0.57018 (14005)

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

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

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 146
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 CYS cc_start: 0.8102 (m) cc_final: 0.7507 (t)
REVERT: A  305 TYR cc_start: 0.6997 (m-80) cc_final: 0.6317 (m-80)
REVERT: A  418 CYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7954 (t)
REVERT: A  466 LYS cc_start: 0.7644 (ttmt) cc_final: 0.7179 (mtpt)
REVERT: A  568 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.5970 (m-80)
REVERT: A  842 MET cc_start: 0.9144 (mmm) cc_final: 0.8876 (tpt)
REVERT: B  110 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7732 (tp30)
  outliers start: 36
  outliers final: 18
  residues processed: 177
  average time/residue: 0.1734
  time to fit residues: 47.8625
Evaluate side-chains
  150 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 PHE
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  568 PHE
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  754 GLU
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain B residue  264 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 9 optimal weight:    8.9990
   chunk 68 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 127 optimal weight:    3.9990
   chunk 106 optimal weight:    0.0070
   chunk 19 optimal weight:    9.9990
   chunk 110 optimal weight:    1.9990
   chunk 114 optimal weight:   40.0000
   chunk 121 optimal weight:    3.9990
   overall best weight:    2.1604

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 554 GLN
A 936 GLN
** G  31 HIS ** 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 = 0.3468 r_free = 0.3468 target = 0.103806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.083122 restraints weight = 22558.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.085679 restraints weight = 11915.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.087409 restraints weight = 7858.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10334  Z= 0.174
  Angle     :  0.615   9.373  14011  Z= 0.307
  Chirality :  0.044   0.209   1579
  Planarity :  0.004   0.047   1804
  Dihedral  :  6.277 123.851   1396
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.32 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.81 %
    Favored  : 70.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.57 (0.24), residues: 1279
  helix:  1.80 (0.23), residues: 560
  sheet: -0.61 (0.46), residues: 137
  loop : -0.77 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  79 
 HIS   0.003   0.001   HIS A 656 
 PHE   0.019   0.001   PHE A 783 
 TYR   0.017   0.002   TYR A 859 
 ARG   0.003   0.000   ARG A 648 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03255 (  474)
  hydrogen bonds       : angle       4.13366 ( 1386)
  SS BOND              : bond        0.00244 (    3)
  SS BOND              : angle       1.36850 (    6)
  covalent geometry    : bond        0.00403 (10331)
  covalent geometry    : angle       0.61424 (14005)

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

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

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 133
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 CYS cc_start: 0.8089 (m) cc_final: 0.7413 (t)
REVERT: A  204 ASP cc_start: 0.8186 (t0) cc_final: 0.7943 (t0)
REVERT: A  305 TYR cc_start: 0.7183 (m-80) cc_final: 0.6360 (m-80)
REVERT: A  418 CYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8009 (t)
REVERT: A  466 LYS cc_start: 0.7689 (ttmt) cc_final: 0.7259 (mtpt)
REVERT: A  568 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6095 (m-80)
REVERT: A  569 THR cc_start: 0.7568 (OUTLIER) cc_final: 0.7302 (p)
REVERT: A  901 ARG cc_start: 0.9101 (ptp90) cc_final: 0.8594 (ptt90)
REVERT: B   87 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6962 (pm20)
REVERT: B  110 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7775 (tp30)
  outliers start: 41
  outliers final: 24
  residues processed: 168
  average time/residue: 0.1677
  time to fit residues: 43.6935
Evaluate side-chains
  152 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 PHE
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  568 PHE
Chi-restraints excluded: chain A residue  569 THR
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  754 GLU
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain B residue   87 GLU
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain B residue  256 GLN
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain G residue   36 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 106 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0000
   chunk 12 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 90 optimal weight:    0.7980
   chunk 118 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 936 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.106201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.085790 restraints weight = 22590.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.088474 restraints weight = 11695.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.090228 restraints weight = 7576.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10334  Z= 0.110
  Angle     :  0.579   8.169  14011  Z= 0.287
  Chirality :  0.042   0.176   1579
  Planarity :  0.004   0.045   1804
  Dihedral  :  6.070 118.361   1396
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.69 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 27.35 %
    Favored  : 70.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.62 (0.24), residues: 1279
  helix:  1.95 (0.23), residues: 553
  sheet: -0.71 (0.46), residues: 143
  loop : -0.80 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  79 
 HIS   0.003   0.001   HIS G  31 
 PHE   0.015   0.001   PHE A 783 
 TYR   0.013   0.001   TYR A 859 
 ARG   0.002   0.000   ARG A 254 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02903 (  474)
  hydrogen bonds       : angle       3.97293 ( 1386)
  SS BOND              : bond        0.00339 (    3)
  SS BOND              : angle       1.26665 (    6)
  covalent geometry    : bond        0.00247 (10331)
  covalent geometry    : angle       0.57864 (14005)

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

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

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 145
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 CYS cc_start: 0.8103 (m) cc_final: 0.7478 (t)
REVERT: A  204 ASP cc_start: 0.8275 (t0) cc_final: 0.8026 (t0)
REVERT: A  305 TYR cc_start: 0.6921 (m-80) cc_final: 0.6292 (m-80)
REVERT: A  418 CYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7834 (t)
REVERT: A  466 LYS cc_start: 0.7618 (ttmt) cc_final: 0.7187 (mtpt)
REVERT: A  568 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6004 (m-80)
REVERT: A  569 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7288 (p)
REVERT: A  754 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6690 (mp0)
REVERT: A  822 MET cc_start: 0.8527 (mmm) cc_final: 0.8195 (tpp)
REVERT: A  842 MET cc_start: 0.9129 (mmm) cc_final: 0.8890 (tpt)
REVERT: B   32 TRP cc_start: 0.6898 (t-100) cc_final: 0.6605 (t-100)
REVERT: B   87 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6926 (pm20)
  outliers start: 29
  outliers final: 14
  residues processed: 169
  average time/residue: 0.1887
  time to fit residues: 50.3477
Evaluate side-chains
  154 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  568 PHE
Chi-restraints excluded: chain A residue  569 THR
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  754 GLU
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain B residue   87 GLU
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  256 GLN
Chi-restraints excluded: chain B residue  264 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 70 optimal weight:    0.2980
   chunk 110 optimal weight:    4.9990
   chunk 125 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 73 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 39 optimal weight:    9.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 476 ASN
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 554 GLN
A 936 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.106616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.086090 restraints weight = 22784.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.088680 restraints weight = 12363.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.090431 restraints weight = 8334.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10334  Z= 0.164
  Angle     :  0.613  10.864  14011  Z= 0.305
  Chirality :  0.043   0.203   1579
  Planarity :  0.004   0.048   1804
  Dihedral  :  6.107 120.774   1396
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.24 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 26.35 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.59 (0.24), residues: 1279
  helix:  1.84 (0.23), residues: 557
  sheet: -0.57 (0.46), residues: 136
  loop : -0.79 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  79 
 HIS   0.005   0.001   HIS A 483 
 PHE   0.019   0.001   PHE A 783 
 TYR   0.016   0.001   TYR A 859 
 ARG   0.003   0.000   ARG A 901 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03171 (  474)
  hydrogen bonds       : angle       4.08798 ( 1386)
  SS BOND              : bond        0.00278 (    3)
  SS BOND              : angle       1.27157 (    6)
  covalent geometry    : bond        0.00384 (10331)
  covalent geometry    : angle       0.61239 (14005)

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

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

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 136
  time to evaluate  : 1.270 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 ASP cc_start: 0.8345 (t0) cc_final: 0.8123 (t0)
REVERT: A  305 TYR cc_start: 0.7069 (m-80) cc_final: 0.6406 (m-80)
REVERT: A  418 CYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7872 (t)
REVERT: A  466 LYS cc_start: 0.7663 (ttmt) cc_final: 0.7438 (tttt)
REVERT: A  568 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6159 (m-80)
REVERT: A  569 THR cc_start: 0.7559 (OUTLIER) cc_final: 0.7279 (p)
REVERT: A  754 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6861 (mp0)
REVERT: A  842 MET cc_start: 0.9132 (mmm) cc_final: 0.8856 (tpt)
REVERT: A  901 ARG cc_start: 0.9041 (ptp90) cc_final: 0.8701 (ptt90)
REVERT: B   87 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6955 (pm20)
REVERT: B  110 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7760 (tp30)
  outliers start: 44
  outliers final: 31
  residues processed: 172
  average time/residue: 0.1773
  time to fit residues: 47.9253
Evaluate side-chains
  165 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 128
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  239 CYS
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  568 PHE
Chi-restraints excluded: chain A residue  569 THR
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain A residue  676 THR
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  754 GLU
Chi-restraints excluded: chain A residue  758 ILE
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  794 THR
Chi-restraints excluded: chain A residue  820 ASP
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain B residue   87 GLU
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  256 GLN
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain G residue   36 THR
Chi-restraints excluded: chain G residue   53 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 122 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   chunk 44 optimal weight:    9.9990
   chunk 109 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 554 GLN
A 936 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.108323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.087830 restraints weight = 22705.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.090485 restraints weight = 12346.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.092268 restraints weight = 8245.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10334  Z= 0.124
  Angle     :  0.613  13.475  14011  Z= 0.303
  Chirality :  0.042   0.238   1579
  Planarity :  0.004   0.046   1804
  Dihedral  :  5.915 116.298   1396
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.85 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 26.99 %
    Favored  : 69.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.65 (0.25), residues: 1279
  helix:  1.91 (0.23), residues: 555
  sheet: -0.58 (0.46), residues: 138
  loop : -0.76 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  79 
 HIS   0.004   0.001   HIS A 483 
 PHE   0.016   0.001   PHE A 783 
 TYR   0.014   0.001   TYR A 859 
 ARG   0.002   0.000   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02942 (  474)
  hydrogen bonds       : angle       3.97549 ( 1386)
  SS BOND              : bond        0.00165 (    3)
  SS BOND              : angle       1.11568 (    6)
  covalent geometry    : bond        0.00286 (10331)
  covalent geometry    : angle       0.61317 (14005)

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

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

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 131
  time to evaluate  : 1.468 
Fit side-chains
   revert: symmetry clash
REVERT: A  418 CYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7822 (t)
REVERT: A  568 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6063 (m-80)
REVERT: A  754 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6838 (mp0)
REVERT: A  842 MET cc_start: 0.9125 (mmm) cc_final: 0.8857 (tpt)
REVERT: B   32 TRP cc_start: 0.6853 (t-100) cc_final: 0.6612 (t-100)
REVERT: B  110 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7733 (tp30)
  outliers start: 40
  outliers final: 27
  residues processed: 163
  average time/residue: 0.1723
  time to fit residues: 43.8184
Evaluate side-chains
  153 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  568 PHE
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  631 VAL
Chi-restraints excluded: chain A residue  676 THR
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  754 GLU
Chi-restraints excluded: chain A residue  758 ILE
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  794 THR
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  256 GLN
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain G residue   36 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 116 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 111 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0270
   chunk 123 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 97 optimal weight:    0.0980
   chunk 98 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 936 GLN

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 = 0.109666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.089299 restraints weight = 22637.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.092013 restraints weight = 12229.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.093769 restraints weight = 8122.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10334  Z= 0.111
  Angle     :  0.618  13.763  14011  Z= 0.303
  Chirality :  0.042   0.234   1579
  Planarity :  0.004   0.048   1804
  Dihedral  :  5.677 106.522   1396
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.77 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 27.62 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.73 (0.25), residues: 1279
  helix:  2.09 (0.23), residues: 548
  sheet: -0.67 (0.45), residues: 148
  loop : -0.77 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A  79 
 HIS   0.003   0.001   HIS G  31 
 PHE   0.021   0.001   PHE A 946 
 TYR   0.014   0.001   TYR A 859 
 ARG   0.002   0.000   ARG B  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02782 (  474)
  hydrogen bonds       : angle       3.94524 ( 1386)
  SS BOND              : bond        0.00150 (    3)
  SS BOND              : angle       1.06271 (    6)
  covalent geometry    : bond        0.00252 (10331)
  covalent geometry    : angle       0.61750 (14005)

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

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

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 143
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 CYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7811 (t)
REVERT: A  568 PHE cc_start: 0.6655 (OUTLIER) cc_final: 0.5907 (m-80)
REVERT: A  754 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6816 (mp0)
REVERT: A  842 MET cc_start: 0.9130 (mmm) cc_final: 0.8846 (tpt)
REVERT: B   32 TRP cc_start: 0.6811 (t-100) cc_final: 0.6607 (t-100)
REVERT: B   87 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6951 (pm20)
REVERT: B  110 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7738 (tp30)
  outliers start: 35
  outliers final: 21
  residues processed: 173
  average time/residue: 0.1728
  time to fit residues: 46.8912
Evaluate side-chains
  158 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 1.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  568 PHE
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  676 THR
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  754 GLU
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain B residue   87 GLU
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  256 GLN
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain G residue   36 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 33 optimal weight:    0.0000
   chunk 97 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 108 optimal weight:   10.0000
   chunk 126 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 63 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 122 optimal weight:    6.9990
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 936 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.109695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.089550 restraints weight = 22528.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.092188 restraints weight = 12128.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.093948 restraints weight = 8031.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10334  Z= 0.112
  Angle     :  0.622  13.679  14011  Z= 0.305
  Chirality :  0.042   0.234   1579
  Planarity :  0.004   0.047   1804
  Dihedral  :  5.331  88.103   1396
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.61 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 28.07 %
    Favored  : 69.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.79 (0.25), residues: 1279
  helix:  2.13 (0.23), residues: 548
  sheet: -0.77 (0.48), residues: 131
  loop : -0.70 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A  79 
 HIS   0.004   0.001   HIS A 483 
 PHE   0.015   0.001   PHE G  30 
 TYR   0.013   0.001   TYR A 859 
 ARG   0.002   0.000   ARG A 901 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02759 (  474)
  hydrogen bonds       : angle       3.95272 ( 1386)
  SS BOND              : bond        0.00164 (    3)
  SS BOND              : angle       1.03568 (    6)
  covalent geometry    : bond        0.00255 (10331)
  covalent geometry    : angle       0.62225 (14005)

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

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

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2558 Ramachandran restraints generated.
    1279 Oldfield, 0 Emsley, 1279 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  329 THR cc_start: 0.9140 (m) cc_final: 0.8697 (t)
REVERT: A  418 CYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7852 (t)
REVERT: A  568 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.5872 (m-80)
REVERT: A  754 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6856 (mp0)
REVERT: A  842 MET cc_start: 0.9142 (mmm) cc_final: 0.8889 (tpt)
REVERT: B  110 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7748 (tp30)
  outliers start: 31
  outliers final: 24
  residues processed: 163
  average time/residue: 0.1679
  time to fit residues: 43.3948
Evaluate side-chains
  156 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 128
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 PHE
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  568 PHE
Chi-restraints excluded: chain A residue  606 VAL
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  720 ILE
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  754 GLU
Chi-restraints excluded: chain A residue  891 SER
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  256 GLN
Chi-restraints excluded: chain B residue  264 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 54 optimal weight:    0.0070
   chunk 82 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.9202

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 866 ASN
A 936 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.109373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.089183 restraints weight = 22503.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.091738 restraints weight = 12186.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.093487 restraints weight = 8114.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10334  Z= 0.120
  Angle     :  0.632  13.898  14011  Z= 0.309
  Chirality :  0.042   0.236   1579
  Planarity :  0.004   0.048   1804
  Dihedral  :  5.046  71.071   1396
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.77 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 28.61 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.79 (0.25), residues: 1279
  helix:  2.13 (0.23), residues: 548
  sheet: -0.75 (0.48), residues: 131
  loop : -0.70 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A  79 
 HIS   0.003   0.001   HIS A 199 
 PHE   0.030   0.001   PHE A 946 
 TYR   0.014   0.001   TYR A 859 
 ARG   0.002   0.000   ARG B  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02763 (  474)
  hydrogen bonds       : angle       3.95012 ( 1386)
  SS BOND              : bond        0.00156 (    3)
  SS BOND              : angle       1.03820 (    6)
  covalent geometry    : bond        0.00278 (10331)
  covalent geometry    : angle       0.63180 (14005)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3592.95 seconds
wall clock time: 63 minutes 22.04 seconds (3802.04 seconds total)