Starting phenix.real_space_refine
on Thu Sep 18 14:55:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d3u_27164/09_2025/8d3u_27164_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d3u_27164/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d3u_27164/09_2025/8d3u_27164_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d3u_27164/09_2025/8d3u_27164_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d3u_27164/09_2025/8d3u_27164.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d3u_27164/09_2025/8d3u_27164.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.40, per 1000 atoms: 0.24
  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: 0.78
  Conformation dependent library (CDL) restraints added in 522.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.43
  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: 1.82

  Time building geometry restraints manager: 1.10 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:             1.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.910
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.570
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.002   0.000   ARG B  27 
 TYR   0.014   0.001   TYR A 859 
 PHE   0.017   0.001   PHE G  44 
 TRP   0.017   0.001   TRP A  79 
 HIS   0.002   0.001   HIS A 656 

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

*********************** 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  : 0.348 
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: 0.0754
  time to fit residues: 15.5439
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  : 0.366 
-------------------------------------------------------------------------------
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 98 optimal weight:    7.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
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 920 GLN
A 936 GLN
B 205 ASN
B 234 ASN
B 241 GLN
B 265 ASN
G  31 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.105123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.084273 restraints weight = 22696.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.087179 restraints weight = 12588.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.088495 restraints weight = 7988.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.088728 restraints weight = 6323.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.088908 restraints weight = 6269.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10334  Z= 0.205
  Angle     :  0.641   9.903  14011  Z= 0.326
  Chirality :  0.044   0.161   1579
  Planarity :  0.005   0.047   1804
  Dihedral  :  6.410 111.052   1404
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.39 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 25.99 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.25), residues: 1279
  helix:  1.67 (0.23), residues: 563
  sheet: -0.54 (0.48), residues: 136
  loop : -0.84 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 877 
 TYR   0.017   0.002   TYR A 859 
 PHE   0.020   0.002   PHE A 783 
 TRP   0.011   0.001   TRP A  79 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (10331)
  covalent geometry    : angle       0.63922 (14005)
  SS BOND              : bond        0.00658 (    3)
  SS BOND              : angle       2.50132 (    6)
  hydrogen bonds       : bond        0.03707 (  474)
  hydrogen bonds       : angle       4.51095 ( 1386)

*********************** 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
  174 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 134
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 CYS cc_start: 0.8167 (m) cc_final: 0.7467 (t)
REVERT: A   90 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7749 (t80)
REVERT: A  305 TYR cc_start: 0.7111 (m-80) cc_final: 0.6451 (m-80)
REVERT: A  430 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7472 (tp)
REVERT: A  568 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.6207 (m-80)
REVERT: G   35 GLN cc_start: 0.8227 (tm-30) cc_final: 0.8023 (tm-30)
  outliers start: 40
  outliers final: 19
  residues processed: 163
  average time/residue: 0.0783
  time to fit residues: 19.8140
Evaluate side-chains
  145 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
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  181 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  272 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  418 CYS
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  568 PHE
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  917 VAL
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  234 ASN
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain G residue   46 VAL
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 80 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 93 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 126 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9980
   chunk 110 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 262 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.105689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.084957 restraints weight = 22676.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.087571 restraints weight = 11900.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.089348 restraints weight = 7786.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.090358 restraints weight = 5858.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.091162 restraints weight = 4925.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1263

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= 0.119
  Angle     :  0.568   8.694  14011  Z= 0.289
  Chirality :  0.042   0.157   1579
  Planarity :  0.004   0.048   1804
  Dihedral  :  6.277 117.944   1396
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.69 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 26.44 %
    Favored  : 70.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.25), residues: 1279
  helix:  1.79 (0.22), residues: 562
  sheet: -0.74 (0.46), residues: 145
  loop : -0.80 (0.27), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 648 
 TYR   0.013   0.001   TYR A 859 
 PHE   0.017   0.001   PHE A 783 
 TRP   0.014   0.001   TRP A  79 
 HIS   0.002   0.000   HIS A 656 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10331)
  covalent geometry    : angle       0.56768 (14005)
  SS BOND              : bond        0.00214 (    3)
  SS BOND              : angle       1.54229 (    6)
  hydrogen bonds       : bond        0.03285 (  474)
  hydrogen bonds       : angle       4.16160 ( 1386)

*********************** 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
  179 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 CYS cc_start: 0.8144 (m) cc_final: 0.7375 (t)
REVERT: A  430 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7460 (tp)
REVERT: A  568 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.6006 (m-80)
REVERT: A  842 MET cc_start: 0.9192 (mmm) cc_final: 0.8890 (tpt)
REVERT: G   35 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7057 (tm-30)
  outliers start: 31
  outliers final: 13
  residues processed: 176
  average time/residue: 0.0788
  time to fit residues: 21.5878
Evaluate side-chains
  142 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 PHE
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  377 THR
Chi-restraints excluded: chain A residue  430 ILE
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  754 GLU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain B residue  264 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 73 optimal weight:    0.3980
   chunk 87 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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**
G  31 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.105769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.085255 restraints weight = 22615.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.087771 restraints weight = 12196.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.089335 restraints weight = 8097.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.090571 restraints weight = 6242.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.091317 restraints weight = 5187.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10334  Z= 0.138
  Angle     :  0.579   9.274  14011  Z= 0.292
  Chirality :  0.042   0.151   1579
  Planarity :  0.004   0.047   1804
  Dihedral  :  6.192 121.226   1396
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.00 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 25.45 %
    Favored  : 70.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.24), residues: 1279
  helix:  1.85 (0.23), residues: 561
  sheet: -0.56 (0.47), residues: 135
  loop : -0.78 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 648 
 TYR   0.015   0.001   TYR A 859 
 PHE   0.022   0.001   PHE A 291 
 TRP   0.016   0.001   TRP A  79 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10331)
  covalent geometry    : angle       0.57888 (14005)
  SS BOND              : bond        0.00235 (    3)
  SS BOND              : angle       1.41038 (    6)
  hydrogen bonds       : bond        0.03117 (  474)
  hydrogen bonds       : angle       4.05316 ( 1386)

*********************** 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
  189 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 146
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 CYS cc_start: 0.8119 (m) cc_final: 0.7518 (t)
REVERT: A  305 TYR cc_start: 0.7012 (m-80) cc_final: 0.6319 (m-80)
REVERT: A  418 CYS cc_start: 0.8236 (t) cc_final: 0.7914 (t)
REVERT: A  430 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7612 (tt)
REVERT: A  568 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.5914 (m-80)
REVERT: A  569 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7221 (p)
REVERT: A  842 MET cc_start: 0.9162 (mmm) cc_final: 0.8852 (tpt)
REVERT: A  901 ARG cc_start: 0.9022 (ptp90) cc_final: 0.8552 (ptt90)
REVERT: B   99 GLU cc_start: 0.7619 (tp30) cc_final: 0.7400 (tp30)
REVERT: B  110 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7696 (tp30)
  outliers start: 43
  outliers final: 20
  residues processed: 181
  average time/residue: 0.0744
  time to fit residues: 21.3573
Evaluate side-chains
  155 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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  183 ILE
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  377 THR
Chi-restraints excluded: chain A residue  430 ILE
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  720 ILE
Chi-restraints excluded: chain A residue  754 GLU
Chi-restraints excluded: chain A residue  784 ILE
Chi-restraints excluded: chain A residue  820 ASP
Chi-restraints excluded: chain A residue  904 VAL
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
Chi-restraints excluded: chain G residue   46 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 116 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0870
   chunk 71 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0020
   chunk 31 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 126 optimal weight:    3.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    0.5968

-------------------------------------------------------------------------------
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
A 554 GLN
A 936 GLN
G  31 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.107353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.087101 restraints weight = 22413.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.089633 restraints weight = 11916.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.091370 restraints weight = 7897.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.092396 restraints weight = 5955.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.093247 restraints weight = 5016.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1815

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= 0.107
  Angle     :  0.569   8.087  14011  Z= 0.285
  Chirality :  0.042   0.190   1579
  Planarity :  0.004   0.047   1804
  Dihedral  :  6.052 118.119   1396
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.61 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 26.08 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.24), residues: 1279
  helix:  1.93 (0.23), residues: 554
  sheet: -0.56 (0.47), residues: 138
  loop : -0.87 (0.26), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 648 
 TYR   0.013   0.001   TYR A 859 
 PHE   0.015   0.001   PHE A 783 
 TRP   0.017   0.001   TRP A  79 
 HIS   0.004   0.001   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (10331)
  covalent geometry    : angle       0.56821 (14005)
  SS BOND              : bond        0.00735 (    3)
  SS BOND              : angle       1.29886 (    6)
  hydrogen bonds       : bond        0.02864 (  474)
  hydrogen bonds       : angle       3.91771 ( 1386)

*********************** 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
  182 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 148
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 CYS cc_start: 0.8034 (m) cc_final: 0.7410 (t)
REVERT: A  204 ASP cc_start: 0.8211 (t0) cc_final: 0.7970 (t0)
REVERT: A  418 CYS cc_start: 0.8190 (t) cc_final: 0.7799 (t)
REVERT: A  430 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7646 (tt)
REVERT: A  568 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.5834 (m-80)
REVERT: A  842 MET cc_start: 0.9175 (mmm) cc_final: 0.8873 (tpt)
REVERT: A  866 ASN cc_start: 0.7961 (m-40) cc_final: 0.7426 (m-40)
REVERT: B   32 TRP cc_start: 0.6861 (t-100) cc_final: 0.6607 (t-100)
REVERT: B   87 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6854 (pm20)
  outliers start: 34
  outliers final: 17
  residues processed: 175
  average time/residue: 0.0718
  time to fit residues: 19.5671
Evaluate side-chains
  154 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
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  183 ILE
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  430 ILE
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  754 GLU
Chi-restraints excluded: chain A residue  784 ILE
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  264 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 70 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 14 optimal weight:    8.9990
   chunk 127 optimal weight:    2.9990
   chunk 102 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 101 optimal weight:    0.1980
   chunk 98 optimal weight:    8.9990
   chunk 97 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.107713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.087225 restraints weight = 22736.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.089868 restraints weight = 11726.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.091675 restraints weight = 7626.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.092735 restraints weight = 5722.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.093518 restraints weight = 4781.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1984

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= 0.108
  Angle     :  0.571   9.265  14011  Z= 0.285
  Chirality :  0.042   0.173   1579
  Planarity :  0.004   0.048   1804
  Dihedral  :  5.886 114.687   1396
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.30 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 25.90 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.24), residues: 1279
  helix:  1.88 (0.23), residues: 556
  sheet: -0.53 (0.46), residues: 138
  loop : -0.82 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 259 
 TYR   0.013   0.001   TYR A 859 
 PHE   0.014   0.001   PHE A 783 
 TRP   0.019   0.001   TRP A  79 
 HIS   0.004   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (10331)
  covalent geometry    : angle       0.57114 (14005)
  SS BOND              : bond        0.00193 (    3)
  SS BOND              : angle       1.10381 (    6)
  hydrogen bonds       : bond        0.02828 (  474)
  hydrogen bonds       : angle       3.88460 ( 1386)

*********************** 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
  187 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 151
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 CYS cc_start: 0.8047 (m) cc_final: 0.7377 (t)
REVERT: A  204 ASP cc_start: 0.8236 (t0) cc_final: 0.7980 (t0)
REVERT: A  418 CYS cc_start: 0.8207 (t) cc_final: 0.7812 (t)
REVERT: A  430 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7621 (tt)
REVERT: A  568 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.5788 (m-80)
REVERT: A  842 MET cc_start: 0.9210 (mmm) cc_final: 0.8890 (tpt)
REVERT: A  866 ASN cc_start: 0.7962 (m-40) cc_final: 0.7541 (m-40)
REVERT: B   32 TRP cc_start: 0.6834 (t-100) cc_final: 0.6568 (t-100)
REVERT: B   87 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6846 (pm20)
  outliers start: 36
  outliers final: 22
  residues processed: 179
  average time/residue: 0.0806
  time to fit residues: 22.4661
Evaluate side-chains
  163 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
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  183 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  430 ILE
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  754 GLU
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 1008 GLU
Chi-restraints excluded: chain B residue   87 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   53 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   chunk 105 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 16 optimal weight:   10.0000
   chunk 119 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 936 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.107379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.086801 restraints weight = 22793.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.089407 restraints weight = 12419.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.090993 restraints weight = 8392.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.092200 restraints weight = 6575.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.092846 restraints weight = 5543.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10334  Z= 0.162
  Angle     :  0.618  11.374  14011  Z= 0.307
  Chirality :  0.043   0.202   1579
  Planarity :  0.004   0.048   1804
  Dihedral  :  5.958 117.767   1396
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.32 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 26.26 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.24), residues: 1279
  helix:  1.89 (0.23), residues: 553
  sheet: -0.44 (0.47), residues: 136
  loop : -0.81 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 901 
 TYR   0.015   0.001   TYR A 859 
 PHE   0.018   0.001   PHE A 783 
 TRP   0.019   0.001   TRP A  79 
 HIS   0.003   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (10331)
  covalent geometry    : angle       0.61768 (14005)
  SS BOND              : bond        0.00242 (    3)
  SS BOND              : angle       1.18716 (    6)
  hydrogen bonds       : bond        0.03137 (  474)
  hydrogen bonds       : angle       4.02410 ( 1386)

*********************** 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
  178 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 139
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 ASP cc_start: 0.8312 (t0) cc_final: 0.8102 (t0)
REVERT: A  305 TYR cc_start: 0.6970 (m-80) cc_final: 0.6390 (m-80)
REVERT: A  418 CYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7866 (t)
REVERT: A  430 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7634 (tt)
REVERT: A  568 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.5990 (m-80)
REVERT: A  754 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6741 (mp0)
REVERT: A  822 MET cc_start: 0.8524 (mmm) cc_final: 0.8138 (tpp)
REVERT: A  842 MET cc_start: 0.9162 (mmm) cc_final: 0.8911 (tpt)
REVERT: A  901 ARG cc_start: 0.9030 (ptp90) cc_final: 0.8699 (ptt90)
REVERT: B   87 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6954 (pm20)
REVERT: B  110 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7725 (tp30)
  outliers start: 39
  outliers final: 26
  residues processed: 169
  average time/residue: 0.0816
  time to fit residues: 21.7035
Evaluate side-chains
  162 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
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  251 THR
Chi-restraints excluded: chain A residue  276 ILE
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  368 THR
Chi-restraints excluded: chain A residue  418 CYS
Chi-restraints excluded: chain A residue  430 ILE
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  720 ILE
Chi-restraints excluded: chain A residue  754 GLU
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   60 THR
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  184 LEU
Chi-restraints excluded: chain B residue  250 LEU
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 126 optimal weight:    5.9990
   chunk 3 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 84 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.108975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.088482 restraints weight = 22499.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.091135 restraints weight = 12312.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.092867 restraints weight = 8305.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.093886 restraints weight = 6405.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.094695 restraints weight = 5478.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10334  Z= 0.123
  Angle     :  0.608  12.547  14011  Z= 0.301
  Chirality :  0.042   0.224   1579
  Planarity :  0.004   0.047   1804
  Dihedral  :  5.775 112.425   1396
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.93 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 26.35 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.24), residues: 1279
  helix:  1.93 (0.23), residues: 551
  sheet: -0.49 (0.47), residues: 138
  loop : -0.78 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 648 
 TYR   0.014   0.001   TYR A 859 
 PHE   0.021   0.001   PHE A 946 
 TRP   0.020   0.001   TRP A  79 
 HIS   0.004   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10331)
  covalent geometry    : angle       0.60790 (14005)
  SS BOND              : bond        0.00173 (    3)
  SS BOND              : angle       1.05357 (    6)
  hydrogen bonds       : bond        0.02962 (  474)
  hydrogen bonds       : angle       3.93958 ( 1386)

*********************** 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
  173 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 135
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 CYS cc_start: 0.8068 (m) cc_final: 0.7543 (t)
REVERT: A  204 ASP cc_start: 0.8287 (t0) cc_final: 0.8073 (t0)
REVERT: A  418 CYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7803 (t)
REVERT: A  430 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7674 (tt)
REVERT: A  568 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.5934 (m-80)
REVERT: A  754 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6702 (mp0)
REVERT: A  822 MET cc_start: 0.8388 (mmm) cc_final: 0.8044 (tpp)
REVERT: A  842 MET cc_start: 0.9149 (mmm) cc_final: 0.8900 (tpt)
REVERT: A  950 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7647 (mm-30)
REVERT: B   87 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6928 (pm20)
REVERT: B  110 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7719 (tp30)
  outliers start: 38
  outliers final: 28
  residues processed: 165
  average time/residue: 0.0734
  time to fit residues: 19.5052
Evaluate side-chains
  163 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
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  169 GLN
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  276 ILE
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  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  430 ILE
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  784 ILE
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  104 ASN
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain G residue   53 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 84 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.3533 r_free = 0.3533 target = 0.107414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.086801 restraints weight = 22675.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.089449 restraints weight = 12418.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.091068 restraints weight = 8321.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.092235 restraints weight = 6514.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.092854 restraints weight = 5514.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10334  Z= 0.155
  Angle     :  0.637  14.023  14011  Z= 0.316
  Chirality :  0.043   0.246   1579
  Planarity :  0.004   0.048   1804
  Dihedral  :  5.691 108.487   1396
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.32 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 26.08 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.61 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.25), residues: 1279
  helix:  1.90 (0.23), residues: 552
  sheet: -0.49 (0.47), residues: 136
  loop : -0.80 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 648 
 TYR   0.015   0.001   TYR A 859 
 PHE   0.018   0.001   PHE A 783 
 TRP   0.021   0.001   TRP A  79 
 HIS   0.003   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (10331)
  covalent geometry    : angle       0.63715 (14005)
  SS BOND              : bond        0.00194 (    3)
  SS BOND              : angle       1.11570 (    6)
  hydrogen bonds       : bond        0.03115 (  474)
  hydrogen bonds       : angle       4.04614 ( 1386)

*********************** 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
  179 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 133
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  418 CYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7868 (t)
REVERT: A  430 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7670 (tt)
REVERT: A  568 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.6098 (m-80)
REVERT: A  569 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7305 (p)
REVERT: A  754 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6856 (mp0)
REVERT: A  822 MET cc_start: 0.8577 (mmm) cc_final: 0.8151 (tpp)
REVERT: A  842 MET cc_start: 0.9154 (mmm) cc_final: 0.8914 (tpt)
REVERT: A  901 ARG cc_start: 0.9001 (ptp90) cc_final: 0.8661 (ptt90)
REVERT: B   87 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6965 (pm20)
REVERT: B  110 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7688 (tp30)
  outliers start: 46
  outliers final: 30
  residues processed: 169
  average time/residue: 0.0762
  time to fit residues: 20.4556
Evaluate side-chains
  161 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 124
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
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  276 ILE
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  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  430 ILE
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  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  784 ILE
Chi-restraints excluded: chain A residue  794 THR
Chi-restraints excluded: chain A residue  820 ASP
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   60 THR
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  250 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 12 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0060
   chunk 78 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 114 optimal weight:    4.9990
   overall best weight:    0.8798

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.108628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.088199 restraints weight = 22349.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.090825 restraints weight = 12135.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.092583 restraints weight = 8139.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.093571 restraints weight = 6270.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.094405 restraints weight = 5357.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10334  Z= 0.120
  Angle     :  0.637  14.157  14011  Z= 0.313
  Chirality :  0.043   0.236   1579
  Planarity :  0.004   0.046   1804
  Dihedral  :  5.441  91.978   1396
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.77 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 27.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.24), residues: 1279
  helix:  2.01 (0.23), residues: 544
  sheet: -0.49 (0.48), residues: 133
  loop : -0.74 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 824 
 TYR   0.014   0.001   TYR A 859 
 PHE   0.016   0.001   PHE A 291 
 TRP   0.023   0.001   TRP A  79 
 HIS   0.003   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10331)
  covalent geometry    : angle       0.63713 (14005)
  SS BOND              : bond        0.00138 (    3)
  SS BOND              : angle       1.01802 (    6)
  hydrogen bonds       : bond        0.02943 (  474)
  hydrogen bonds       : angle       3.99780 ( 1386)

********************** 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
  164 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 CYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7816 (t)
REVERT: A  430 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7671 (tt)
REVERT: A  473 ASN cc_start: 0.8264 (t0) cc_final: 0.7972 (m-40)
REVERT: A  568 PHE cc_start: 0.6696 (OUTLIER) cc_final: 0.6003 (m-80)
REVERT: A  754 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6935 (mp0)
REVERT: A  822 MET cc_start: 0.8395 (mmm) cc_final: 0.8110 (tpp)
REVERT: A  842 MET cc_start: 0.9148 (mmm) cc_final: 0.8911 (tpt)
REVERT: B   87 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6929 (pm20)
REVERT: B  110 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7699 (tp30)
  outliers start: 33
  outliers final: 25
  residues processed: 159
  average time/residue: 0.0751
  time to fit residues: 19.1372
Evaluate side-chains
  157 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
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  303 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  430 ILE
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  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   87 GLU
Chi-restraints excluded: chain B residue  104 ASN
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain B residue  250 LEU
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 119 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 124 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   chunk 125 optimal weight:   10.0000
   chunk 86 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 94 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 936 GLN
B 212 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.103612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.082247 restraints weight = 22986.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.084877 restraints weight = 12327.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.086651 restraints weight = 8246.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.087655 restraints weight = 6334.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.088485 restraints weight = 5381.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10334  Z= 0.215
  Angle     :  0.693  13.816  14011  Z= 0.346
  Chirality :  0.045   0.255   1579
  Planarity :  0.004   0.048   1804
  Dihedral  :  5.430  73.243   1396
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.18 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 27.80 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.24), residues: 1279
  helix:  1.72 (0.23), residues: 554
  sheet: -0.67 (0.46), residues: 135
  loop : -0.83 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 901 
 TYR   0.019   0.002   TYR G  34 
 PHE   0.022   0.002   PHE A 783 
 TRP   0.018   0.001   TRP A  79 
 HIS   0.005   0.001   HIS A 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (10331)
  covalent geometry    : angle       0.69289 (14005)
  SS BOND              : bond        0.00254 (    3)
  SS BOND              : angle       1.29622 (    6)
  hydrogen bonds       : bond        0.03514 (  474)
  hydrogen bonds       : angle       4.33385 ( 1386)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1876.24 seconds
wall clock time: 33 minutes 11.57 seconds (1991.57 seconds total)