Starting phenix.real_space_refine
on Fri Aug 22 21:57:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ies_35392/08_2025/8ies_35392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ies_35392/08_2025/8ies_35392.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ies_35392/08_2025/8ies_35392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ies_35392/08_2025/8ies_35392.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ies_35392/08_2025/8ies_35392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ies_35392/08_2025/8ies_35392.map"
  }
  resolution = 3.73
  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=   0.002 sd=   0.056
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       2      5.49       5
     Mg      1      5.21       5
     S      53      5.16       5
     C    5129      2.51       5
     N    1367      2.21       5
     O    1408      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 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7965
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "P"
      Number of atoms: 7932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1026, 7932
          Classifications: {'peptide': 1026}
          Link IDs: {'PTRANS': 69, 'TRANS': 956}
          Chain breaks: 4
    Chain: "P"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.61, per 1000 atoms: 0.20
  Number of scatterers: 7965
  At special positions: 0
  Unit cell: (96.36, 91.98, 131.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      53     16.00
     P       2     15.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1408      8.00
     N    1367      7.00
     C    5129      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 279.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 8 sheets defined
      41.2% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'P' and resid 49 through 58
      removed outlier: 4.344A  pdb=" N   VAL P  53 " --> pdb=" O   GLY P  49 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   TRP P  55 " --> pdb=" O   HIS P  51 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 59 through 64
      removed outlier: 3.555A  pdb=" N   LEU P  62 " --> pdb=" O   GLY P  59 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU P  63 " --> pdb=" O   ILE P  60 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 69 through 76
      removed outlier: 3.592A  pdb=" N   VAL P  73 " --> pdb=" O   PRO P  69 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 194 through 199
    Processing helix  chain 'P' and resid 227 through 234
      removed outlier: 3.925A  pdb=" N   ASP P 234 " --> pdb=" O   GLN P 230 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 238 through 253
      removed outlier: 3.586A  pdb=" N   GLY P 242 " --> pdb=" O   ASN P 238 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 258 through 287
      removed outlier: 3.934A  pdb=" N   LEU P 285 " --> pdb=" O   GLN P 281 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 402 through 412
    Processing helix  chain 'P' and resid 423 through 450
      removed outlier: 3.792A  pdb=" N   LYS P 427 " --> pdb=" O   LYS P 423 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 456 through 467
      removed outlier: 4.015A  pdb=" N   ARG P 460 " --> pdb=" O   GLU P 456 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 472 through 478
      removed outlier: 3.507A  pdb=" N   MET P 477 " --> pdb=" O   LEU P 473 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   THR P 478 " --> pdb=" O   PRO P 474 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 478 through 489
      removed outlier: 3.984A  pdb=" N   LEU P 482 " --> pdb=" O   THR P 478 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ARG P 489 " --> pdb=" O   GLN P 485 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 503 through 507
      removed outlier: 3.621A  pdb=" N   LEU P 507 " --> pdb=" O   GLY P 504 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 550 through 557
    Processing helix  chain 'P' and resid 571 through 580
    Processing helix  chain 'P' and resid 609 through 612
    Processing helix  chain 'P' and resid 656 through 662
      removed outlier: 4.256A  pdb=" N   GLY P 662 " --> pdb=" O   GLU P 658 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 672 through 682
      removed outlier: 3.737A  pdb=" N   GLN P 678 " --> pdb=" O   ALA P 674 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 696 through 704
      removed outlier: 3.548A  pdb=" N   ALA P 704 " --> pdb=" O   SER P 700 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 732 through 741
    Processing helix  chain 'P' and resid 753 through 765
      removed outlier: 3.874A  pdb=" N   CYS P 764 " --> pdb=" O   VAL P 760 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 826 through 832
    Processing helix  chain 'P' and resid 840 through 847
      removed outlier: 3.559A  pdb=" N   VAL P 844 " --> pdb=" O   LEU P 840 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   VAL P 846 " --> pdb=" O   PRO P 842 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   GLN P 847 " --> pdb=" O   LYS P 843 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 858 through 868
    Processing helix  chain 'P' and resid 882 through 887
      removed outlier: 3.932A  pdb=" N   LEU P 886 " --> pdb=" O   ASP P 882 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LYS P 887 " --> pdb=" O   CYS P 883 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 882 through 887'
    Processing helix  chain 'P' and resid 915 through 952
    Processing helix  chain 'P' and resid 959 through 969
      removed outlier: 4.052A  pdb=" N   PHE P 963 " --> pdb=" O   GLY P 959 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LEU P 964 " --> pdb=" O   ASP P 960 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 971 through 977
    Processing helix  chain 'P' and resid 998 through 1025
    Processing helix  chain 'P' and resid 1046 through 1066
      removed outlier: 4.159A  pdb=" N   VAL P1050 " --> pdb=" O   GLU P1046 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   PHE P1056 " --> pdb=" O   SER P1052 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLN P1057 " --> pdb=" O   LEU P1053 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   TYR P1058 " --> pdb=" O   SER P1054 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   LEU P1059 " --> pdb=" O   SER P1055 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA P1063 " --> pdb=" O   LEU P1059 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL P1065 " --> pdb=" O   LEU P1061 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   SER P1066 " --> pdb=" O   ALA P1062 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1078 through 1094
    Processing helix  chain 'P' and resid 1117 through 1136
      removed outlier: 4.148A  pdb=" N   LEU P1123 " --> pdb=" O   LEU P1119 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   PHE P1132 " --> pdb=" O   PHE P1128 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1141 through 1147
    Processing helix  chain 'P' and resid 1157 through 1167
    Processing sheet with id=AA1, first strand: chain 'P' and resid 39 through 43
      removed outlier: 4.355A  pdb=" N   GLY P  39 " --> pdb=" O   ILE P  92 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE P  92 " --> pdb=" O   GLY P  39 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU P  88 " --> pdb=" O   SER P  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'P' and resid 105 through 106
      removed outlier: 6.495A  pdb=" N   ARG P 164 " --> pdb=" O   TRP P 175 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   TRP P 175 " --> pdb=" O   ARG P 164 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   TYR P 166 " --> pdb=" O   TYR P 173 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   TYR P 173 " --> pdb=" O   TYR P 166 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'P' and resid 297 through 298
      removed outlier: 4.028A  pdb=" N   VAL P 297 " --> pdb=" O   GLU P 305 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   GLU P 305 " --> pdb=" O   VAL P 297 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'P' and resid 317 through 318
      removed outlier: 3.616A  pdb=" N   ALA P 393 " --> pdb=" O   LEU P 318 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   LEU P 392 " --> pdb=" O   VAL P 334 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL P 334 " --> pdb=" O   LEU P 392 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'P' and resid 338 through 340
    Processing sheet with id=AA6, first strand: chain 'P' and resid 823 through 825
      removed outlier: 6.237A  pdb=" N   LEU P 823 " --> pdb=" O   GLY P 848 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   VAL P 850 " --> pdb=" O   LEU P 823 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   ALA P 746 " --> pdb=" O   THR P 849 " (cutoff:3.500A)
      removed outlier: 9.148A  pdb=" N   PHE P 851 " --> pdb=" O   ALA P 746 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   MET P 748 " --> pdb=" O   PHE P 851 " (cutoff:3.500A)
      removed outlier: 9.141A  pdb=" N   ILE P 893 " --> pdb=" O   VAL P 873 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   MET P 875 " --> pdb=" O   ILE P 893 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'P' and resid 528 through 530
      removed outlier: 5.119A  pdb=" N   LEU P 718 " --> pdb=" O   SER P 692 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   SER P 692 " --> pdb=" O   LEU P 718 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   GLY P 720 " --> pdb=" O   LEU P 690 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU P 722 " --> pdb=" O   VAL P 688 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA P 651 " --> pdb=" O   LYS P 693 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   HIS P 626 " --> pdb=" O   VAL P 640 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ALA P 642 " --> pdb=" O   VAL P 624 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   VAL P 624 " --> pdb=" O   ALA P 642 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'P' and resid 584 through 586
      removed outlier: 4.073A  pdb=" N   VAL P 584 " --> pdb=" O   MET P 615 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLN P 613 " --> pdb=" O   GLU P 586 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    873 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: 1.07

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2557
        1.34 -     1.46: 1664
        1.46 -     1.58: 3832
        1.58 -     1.69: 3
        1.69 -     1.81: 83
  Bond restraints: 8139
  Sorted by residual:
  bond pdb=" F1  ALF P1201 "
       pdb="AL   ALF P1201 "
    ideal  model  delta    sigma   weight residual
    1.684  1.785 -0.101 2.00e-02 2.50e+03 2.57e+01
  bond pdb=" F2  ALF P1201 "
       pdb="AL   ALF P1201 "
    ideal  model  delta    sigma   weight residual
    1.685  1.785 -0.100 2.00e-02 2.50e+03 2.50e+01
  bond pdb=" F3  ALF P1201 "
       pdb="AL   ALF P1201 "
    ideal  model  delta    sigma   weight residual
    1.685  1.784 -0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" F4  ALF P1201 "
       pdb="AL   ALF P1201 "
    ideal  model  delta    sigma   weight residual
    1.686  1.785 -0.099 2.00e-02 2.50e+03 2.46e+01
  bond pdb=" C   LEU P1142 "
       pdb=" N   PRO P1143 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.020 1.28e-02 6.10e+03 2.52e+00
  ... (remaining 8134 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.25: 11088
       14.25 -    28.50: 4
       28.50 -    42.75: 0
       42.75 -    56.99: 0
       56.99 -    71.24: 2
  Bond angle restraints: 11094
  Sorted by residual:
  angle pdb=" F1  ALF P1201 "
        pdb="AL   ALF P1201 "
        pdb=" F2  ALF P1201 "
      ideal   model   delta    sigma   weight residual
     108.68  179.92  -71.24 3.00e+00 1.11e-01 5.64e+02
  angle pdb=" F3  ALF P1201 "
        pdb="AL   ALF P1201 "
        pdb=" F4  ALF P1201 "
      ideal   model   delta    sigma   weight residual
     109.63  179.96  -70.33 3.00e+00 1.11e-01 5.50e+02
  angle pdb=" F2  ALF P1201 "
        pdb="AL   ALF P1201 "
        pdb=" F4  ALF P1201 "
      ideal   model   delta    sigma   weight residual
     110.21   89.99   20.22 3.00e+00 1.11e-01 4.54e+01
  angle pdb=" F1  ALF P1201 "
        pdb="AL   ALF P1201 "
        pdb=" F3  ALF P1201 "
      ideal   model   delta    sigma   weight residual
     109.69   89.98   19.71 3.00e+00 1.11e-01 4.32e+01
  angle pdb=" F2  ALF P1201 "
        pdb="AL   ALF P1201 "
        pdb=" F3  ALF P1201 "
      ideal   model   delta    sigma   weight residual
     109.59   90.02   19.57 3.00e+00 1.11e-01 4.25e+01
  ... (remaining 11089 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.02: 4699
       27.02 -    54.05: 204
       54.05 -    81.07: 10
       81.07 -   108.10: 0
      108.10 -   135.12: 3
  Dihedral angle restraints: 4916
    sinusoidal: 1948
      harmonic: 2968
  Sorted by residual:
  dihedral pdb=" O2A ADP P1203 "
           pdb=" O3A ADP P1203 "
           pdb=" PA  ADP P1203 "
           pdb=" PB  ADP P1203 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   75.12 -135.12     1      2.00e+01 2.50e-03 4.10e+01
  dihedral pdb=" C5' ADP P1203 "
           pdb=" O5' ADP P1203 "
           pdb=" PA  ADP P1203 "
           pdb=" O2A ADP P1203 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   67.58 -127.57     1      2.00e+01 2.50e-03 3.86e+01
  dihedral pdb=" O1B ADP P1203 "
           pdb=" O3A ADP P1203 "
           pdb=" PB  ADP P1203 "
           pdb=" PA  ADP P1203 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   66.52 -126.52     1      2.00e+01 2.50e-03 3.83e+01
  ... (remaining 4913 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 754
       0.026 -    0.053: 351
       0.053 -    0.079: 116
       0.079 -    0.105: 78
       0.105 -    0.132: 19
  Chirality restraints: 1318
  Sorted by residual:
  chirality pdb=" CA  ILE P 350 "
            pdb=" N   ILE P 350 "
            pdb=" C   ILE P 350 "
            pdb=" CB  ILE P 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  VAL P 469 "
            pdb=" N   VAL P 469 "
            pdb=" C   VAL P 469 "
            pdb=" CB  VAL P 469 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.00e-01
  chirality pdb=" CA  VAL P 313 "
            pdb=" N   VAL P 313 "
            pdb=" C   VAL P 313 "
            pdb=" CB  VAL P 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.69e-01
  ... (remaining 1315 not shown)

  Planarity restraints: 1395
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU P 617 "   -0.025 5.00e-02 4.00e+02   3.79e-02 2.30e+00
        pdb=" N   PRO P 618 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO P 618 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO P 618 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL P 999 "    0.019 5.00e-02 4.00e+02   2.82e-02 1.27e+00
        pdb=" N   PRO P1000 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO P1000 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO P1000 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR P 567 "    0.018 5.00e-02 4.00e+02   2.65e-02 1.13e+00
        pdb=" N   PRO P 568 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO P 568 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO P 568 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1392 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1960
        2.79 -     3.32: 6981
        3.32 -     3.85: 12303
        3.85 -     4.37: 12953
        4.37 -     4.90: 23214
  Nonbonded interactions: 57411
  Sorted by model distance:
  nonbonded pdb=" O   THR P 515 "
            pdb=" F2  ALF P1201 "
     model   vdw
     2.268 2.990
  nonbonded pdb=" N   GLY P 879 "
            pdb="MG    MG P1202 "
     model   vdw
     2.270 2.250
  nonbonded pdb=" O   ARG P 553 "
            pdb=" OG1 THR P 557 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG1 THR P 647 "
            pdb=" OE1 GLN P 648 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   ASP P 967 "
            pdb=" OG1 THR P 972 "
     model   vdw
     2.309 3.040
  ... (remaining 57406 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.310
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6520
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.101   8140  Z= 0.151
  Angle     :  1.160  71.242  11094  Z= 0.454
  Chirality :  0.039   0.132   1318
  Planarity :  0.003   0.038   1395
  Dihedral  : 13.702 135.121   3000
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.84 (0.22), residues: 1016
  helix: -0.87 (0.24), residues: 396
  sheet: -2.51 (0.53), residues: 79
  loop : -4.08 (0.19), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG P 201 
 TYR   0.003   0.000   TYR P 241 
 PHE   0.003   0.000   PHE P1128 
 TRP   0.007   0.000   TRP P  55 
 HIS   0.001   0.000   HIS P  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8139)
  covalent geometry    : angle       1.15972 (11094)
  hydrogen bonds       : bond        0.16574 (  300)
  hydrogen bonds       : angle       6.21523 (  873)
  Misc. bond           : bond        0.00050 (    1)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: P   40 TYR cc_start: 0.4402 (m-80) cc_final: 0.3239 (m-80)
REVERT: P  437 LEU cc_start: 0.8732 (pp) cc_final: 0.8468 (mp)
REVERT: P  641 VAL cc_start: 0.8123 (t) cc_final: 0.7742 (p)
REVERT: P  942 LEU cc_start: 0.9024 (tp) cc_final: 0.8573 (tp)
REVERT: P 1012 VAL cc_start: 0.7641 (t) cc_final: 0.7412 (t)
REVERT: P 1046 GLU cc_start: 0.7213 (mp0) cc_final: 0.6795 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.0987
  time to fit residues: 25.8669
Evaluate side-chains
  119 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0570
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.1102

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

Flipped N/Q/H residues before XYZ refinement:
P  51 HIS
P  84 HIS
** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 534 GLN
P 755 GLN
P 822 HIS
P 858 GLN
P1026 GLN
P1033 ASN
P1169 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.161951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.130838 restraints weight = 16824.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.134096 restraints weight = 10843.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.135836 restraints weight = 8002.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.136309 restraints weight = 6506.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.136661 restraints weight = 6273.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8140  Z= 0.184
  Angle     :  0.978  31.994  11094  Z= 0.410
  Chirality :  0.045   0.172   1318
  Planarity :  0.005   0.044   1395
  Dihedral  :  6.853 132.899   1125
  Min Nonbonded Distance : 1.633

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.96 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.03 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.64 (0.25), residues: 1016
  helix:  0.55 (0.28), residues: 389
  sheet: -2.52 (0.51), residues: 81
  loop : -3.59 (0.21), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG P 627 
 TYR   0.024   0.002   TYR P 241 
 PHE   0.015   0.002   PHE P 512 
 TRP   0.031   0.003   TRP P  55 
 HIS   0.007   0.001   HIS P 780 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 8139)
  covalent geometry    : angle       0.97838 (11094)
  hydrogen bonds       : bond        0.03621 (  300)
  hydrogen bonds       : angle       4.11272 (  873)
  Misc. bond           : bond        0.00323 (    1)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  267 SER cc_start: 0.7733 (m) cc_final: 0.7446 (p)
REVERT: P  437 LEU cc_start: 0.8731 (pp) cc_final: 0.8443 (mp)
REVERT: P  893 ILE cc_start: 0.8517 (mm) cc_final: 0.7755 (mm)
REVERT: P 1046 GLU cc_start: 0.7461 (mp0) cc_final: 0.7125 (mp0)
  outliers start: 20
  outliers final: 11
  residues processed: 159
  average time/residue: 0.0988
  time to fit residues: 21.1380
Evaluate side-chains
  121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  278 THR
Chi-restraints excluded: chain P residue  373 THR
Chi-restraints excluded: chain P residue  408 VAL
Chi-restraints excluded: chain P residue  434 VAL
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  634 LEU
Chi-restraints excluded: chain P residue  735 VAL
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  946 ILE
Chi-restraints excluded: chain P residue  986 VAL
Chi-restraints excluded: chain P residue 1138 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   chunk 100 optimal weight:    0.0020
   chunk 80 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0970
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
P 413 HIS
P 491 GLN
P1057 GLN
P1127 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.160898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.129480 restraints weight = 16663.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.133137 restraints weight = 10043.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.135517 restraints weight = 7248.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.137107 restraints weight = 5850.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.137919 restraints weight = 5075.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8140  Z= 0.111
  Angle     :  0.903  30.184  11094  Z= 0.363
  Chirality :  0.042   0.172   1318
  Planarity :  0.005   0.054   1395
  Dihedral  :  6.478 133.647   1125
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 18.68 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.13 (0.26), residues: 1016
  helix:  1.06 (0.29), residues: 388
  sheet: -1.82 (0.60), residues: 75
  loop : -3.43 (0.22), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG P 740 
 TYR   0.013   0.001   TYR P 241 
 PHE   0.022   0.001   PHE P 445 
 TRP   0.025   0.002   TRP P  45 
 HIS   0.004   0.001   HIS P 822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8139)
  covalent geometry    : angle       0.90297 (11094)
  hydrogen bonds       : bond        0.02978 (  300)
  hydrogen bonds       : angle       3.75036 (  873)
  Misc. bond           : bond        0.00151 (    1)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.320 
Fit side-chains
REVERT: P  267 SER cc_start: 0.7768 (m) cc_final: 0.7527 (p)
REVERT: P  437 LEU cc_start: 0.8725 (pp) cc_final: 0.8379 (mp)
REVERT: P  573 MET cc_start: 0.6818 (ttm) cc_final: 0.6329 (ttt)
REVERT: P  766 MET cc_start: 0.3294 (pmm) cc_final: 0.2737 (ptp)
REVERT: P  893 ILE cc_start: 0.8766 (mm) cc_final: 0.8080 (mm)
REVERT: P 1046 GLU cc_start: 0.7356 (mp0) cc_final: 0.7109 (mp0)
  outliers start: 15
  outliers final: 7
  residues processed: 131
  average time/residue: 0.0846
  time to fit residues: 15.9060
Evaluate side-chains
  112 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  424 HIS
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  634 LEU
Chi-restraints excluded: chain P residue  735 VAL
Chi-restraints excluded: chain P residue  871 TYR
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue 1138 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 65 optimal weight:    0.4980
   chunk 93 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0270
   chunk 6 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.5840

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

Flipped N/Q/H residues before XYZ refinement:
** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.157311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.126141 restraints weight = 16966.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.129481 restraints weight = 10353.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.130487 restraints weight = 8115.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.131040 restraints weight = 6990.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.131507 restraints weight = 6385.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.4714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8140  Z= 0.117
  Angle     :  0.889  30.842  11094  Z= 0.357
  Chirality :  0.042   0.134   1318
  Planarity :  0.004   0.050   1395
  Dihedral  :  6.189 122.363   1125
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.58 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 21.07 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.27), residues: 1016
  helix:  1.06 (0.29), residues: 396
  sheet: -1.78 (0.57), residues: 81
  loop : -3.28 (0.22), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG P  76 
 TYR   0.023   0.001   TYR P 183 
 PHE   0.017   0.001   PHE P 494 
 TRP   0.017   0.002   TRP P  45 
 HIS   0.002   0.001   HIS P 836 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8139)
  covalent geometry    : angle       0.88912 (11094)
  hydrogen bonds       : bond        0.02902 (  300)
  hydrogen bonds       : angle       3.67077 (  873)
  Misc. bond           : bond        0.00200 (    1)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.337 
Fit side-chains
REVERT: P  293 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6421 (ptp)
REVERT: P  437 LEU cc_start: 0.8676 (pp) cc_final: 0.8357 (mp)
REVERT: P  573 MET cc_start: 0.6933 (ttm) cc_final: 0.6603 (ttt)
REVERT: P  766 MET cc_start: 0.2981 (OUTLIER) cc_final: 0.2162 (ptp)
REVERT: P  861 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7291 (tp30)
REVERT: P  893 ILE cc_start: 0.8689 (mm) cc_final: 0.8430 (mm)
REVERT: P 1046 GLU cc_start: 0.7309 (mp0) cc_final: 0.7073 (mp0)
  outliers start: 16
  outliers final: 13
  residues processed: 130
  average time/residue: 0.0895
  time to fit residues: 16.4393
Evaluate side-chains
  117 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  293 MET
Chi-restraints excluded: chain P residue  318 LEU
Chi-restraints excluded: chain P residue  424 HIS
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  634 LEU
Chi-restraints excluded: chain P residue  687 VAL
Chi-restraints excluded: chain P residue  735 VAL
Chi-restraints excluded: chain P residue  759 THR
Chi-restraints excluded: chain P residue  766 MET
Chi-restraints excluded: chain P residue  773 LEU
Chi-restraints excluded: chain P residue  871 TYR
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  903 VAL
Chi-restraints excluded: chain P residue  986 VAL
Chi-restraints excluded: chain P residue 1138 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 85 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 95 optimal weight:    0.3980
   chunk 98 optimal weight:    6.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
P  81 ASN
P 753 ASN
** P1033 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.143895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.113687 restraints weight = 16600.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.113882 restraints weight = 11666.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.114828 restraints weight = 9968.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.115539 restraints weight = 8461.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.115849 restraints weight = 7935.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.6497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   8140  Z= 0.237
  Angle     :  1.020  33.910  11094  Z= 0.439
  Chirality :  0.048   0.206   1318
  Planarity :  0.005   0.047   1395
  Dihedral  :  6.499 107.128   1125
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.45 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 22.78 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.12 (0.26), residues: 1016
  helix:  0.68 (0.28), residues: 403
  sheet: -1.91 (0.54), residues: 85
  loop : -3.19 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG P 989 
 TYR   0.012   0.002   TYR P 276 
 PHE   0.018   0.002   PHE P1021 
 TRP   0.019   0.002   TRP P  45 
 HIS   0.008   0.002   HIS P 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 8139)
  covalent geometry    : angle       1.02047 (11094)
  hydrogen bonds       : bond        0.04585 (  300)
  hydrogen bonds       : angle       4.17402 (  873)
  Misc. bond           : bond        0.00368 (    1)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 106
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: P   84 HIS cc_start: 0.7853 (t-90) cc_final: 0.7630 (t-170)
REVERT: P  243 PHE cc_start: 0.8417 (t80) cc_final: 0.8198 (t80)
REVERT: P  293 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6944 (ptp)
REVERT: P  748 MET cc_start: 0.8530 (ttp) cc_final: 0.8263 (ttt)
REVERT: P  766 MET cc_start: 0.3680 (OUTLIER) cc_final: 0.3025 (ptp)
REVERT: P  861 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7640 (tp30)
REVERT: P  865 GLU cc_start: 0.7968 (tp30) cc_final: 0.7452 (tp30)
REVERT: P  894 SER cc_start: 0.9050 (m) cc_final: 0.8562 (t)
  outliers start: 35
  outliers final: 17
  residues processed: 133
  average time/residue: 0.0827
  time to fit residues: 15.7721
Evaluate side-chains
  121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  293 MET
Chi-restraints excluded: chain P residue  334 VAL
Chi-restraints excluded: chain P residue  424 HIS
Chi-restraints excluded: chain P residue  434 VAL
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  496 ILE
Chi-restraints excluded: chain P residue  551 LEU
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  687 VAL
Chi-restraints excluded: chain P residue  735 VAL
Chi-restraints excluded: chain P residue  759 THR
Chi-restraints excluded: chain P residue  766 MET
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  903 VAL
Chi-restraints excluded: chain P residue  933 VAL
Chi-restraints excluded: chain P residue  978 MET
Chi-restraints excluded: chain P residue  986 VAL
Chi-restraints excluded: chain P residue 1149 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 96 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** P 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.146090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.114194 restraints weight = 16431.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.117383 restraints weight = 10328.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.118134 restraints weight = 7681.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.118548 restraints weight = 6801.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.118769 restraints weight = 6472.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.6659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8140  Z= 0.134
  Angle     :  0.925  30.524  11094  Z= 0.379
  Chirality :  0.043   0.146   1318
  Planarity :  0.005   0.059   1395
  Dihedral  :  5.866  97.793   1125
  Min Nonbonded Distance : 1.837

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 24.94 %
    Favored  : 71.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.27), residues: 1016
  helix:  1.03 (0.28), residues: 401
  sheet: -1.81 (0.56), residues: 80
  loop : -3.00 (0.23), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P 745 
 TYR   0.011   0.001   TYR P 241 
 PHE   0.008   0.001   PHE P1021 
 TRP   0.015   0.001   TRP P  45 
 HIS   0.002   0.001   HIS P 772 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8139)
  covalent geometry    : angle       0.92522 (11094)
  hydrogen bonds       : bond        0.03549 (  300)
  hydrogen bonds       : angle       3.80429 (  873)
  Misc. bond           : bond        0.00166 (    1)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: P   84 HIS cc_start: 0.7864 (t-90) cc_final: 0.7633 (t-170)
REVERT: P  293 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6811 (ptp)
REVERT: P  766 MET cc_start: 0.3995 (OUTLIER) cc_final: 0.3127 (ptp)
REVERT: P  861 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7590 (tp30)
REVERT: P  865 GLU cc_start: 0.7644 (tp30) cc_final: 0.7276 (tp30)
REVERT: P  894 SER cc_start: 0.8898 (m) cc_final: 0.8364 (t)
REVERT: P 1046 GLU cc_start: 0.7346 (mp0) cc_final: 0.7017 (mp0)
  outliers start: 28
  outliers final: 15
  residues processed: 127
  average time/residue: 0.0843
  time to fit residues: 15.3554
Evaluate side-chains
  122 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  293 MET
Chi-restraints excluded: chain P residue  355 THR
Chi-restraints excluded: chain P residue  424 HIS
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  551 LEU
Chi-restraints excluded: chain P residue  622 VAL
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  735 VAL
Chi-restraints excluded: chain P residue  736 ILE
Chi-restraints excluded: chain P residue  759 THR
Chi-restraints excluded: chain P residue  766 MET
Chi-restraints excluded: chain P residue  871 TYR
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  903 VAL
Chi-restraints excluded: chain P residue  978 MET
Chi-restraints excluded: chain P residue 1091 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0020
   chunk 53 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
P 491 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.147621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.117921 restraints weight = 16330.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.119688 restraints weight = 11246.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.121301 restraints weight = 8132.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.122111 restraints weight = 6878.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.122694 restraints weight = 6423.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.6818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8140  Z= 0.128
  Angle     :  0.931  30.499  11094  Z= 0.381
  Chirality :  0.043   0.145   1318
  Planarity :  0.005   0.074   1395
  Dihedral  :  5.627  97.221   1125
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 25.63 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.60 (0.27), residues: 1016
  helix:  1.18 (0.29), residues: 401
  sheet: -1.66 (0.58), residues: 77
  loop : -2.92 (0.24), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P 745 
 TYR   0.018   0.001   TYR P 183 
 PHE   0.014   0.001   PHE P1159 
 TRP   0.019   0.002   TRP P 100 
 HIS   0.002   0.001   HIS P 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8139)
  covalent geometry    : angle       0.93104 (11094)
  hydrogen bonds       : bond        0.03389 (  300)
  hydrogen bonds       : angle       3.77480 (  873)
  Misc. bond           : bond        0.00163 (    1)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: P   84 HIS cc_start: 0.7859 (t-90) cc_final: 0.7621 (t-170)
REVERT: P  293 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6671 (ptp)
REVERT: P  766 MET cc_start: 0.4052 (OUTLIER) cc_final: 0.3060 (ptp)
REVERT: P  861 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7629 (tp30)
REVERT: P  865 GLU cc_start: 0.7692 (tp30) cc_final: 0.7286 (tp30)
REVERT: P  894 SER cc_start: 0.8798 (m) cc_final: 0.8300 (t)
REVERT: P 1046 GLU cc_start: 0.7243 (mp0) cc_final: 0.6902 (mp0)
  outliers start: 27
  outliers final: 16
  residues processed: 125
  average time/residue: 0.0827
  time to fit residues: 14.8533
Evaluate side-chains
  121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  293 MET
Chi-restraints excluded: chain P residue  353 LEU
Chi-restraints excluded: chain P residue  355 THR
Chi-restraints excluded: chain P residue  424 HIS
Chi-restraints excluded: chain P residue  435 LEU
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  551 LEU
Chi-restraints excluded: chain P residue  622 VAL
Chi-restraints excluded: chain P residue  637 MET
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  735 VAL
Chi-restraints excluded: chain P residue  736 ILE
Chi-restraints excluded: chain P residue  759 THR
Chi-restraints excluded: chain P residue  766 MET
Chi-restraints excluded: chain P residue  871 TYR
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  903 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 80 optimal weight:    0.5980
   chunk 93 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 101 optimal weight:    0.0050
   chunk 17 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
P 491 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.148242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.118895 restraints weight = 16372.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.120885 restraints weight = 10403.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.121904 restraints weight = 8203.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.122287 restraints weight = 6854.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.122543 restraints weight = 6486.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.6922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8140  Z= 0.117
  Angle     :  0.911  30.212  11094  Z= 0.371
  Chirality :  0.043   0.148   1318
  Planarity :  0.005   0.066   1395
  Dihedral  :  5.457  98.588   1125
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 26.08 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.27), residues: 1016
  helix:  1.17 (0.28), residues: 406
  sheet: -1.45 (0.62), residues: 72
  loop : -2.85 (0.23), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P 745 
 TYR   0.009   0.001   TYR P 241 
 PHE   0.016   0.001   PHE P1159 
 TRP   0.019   0.001   TRP P  45 
 HIS   0.002   0.000   HIS P 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8139)
  covalent geometry    : angle       0.91127 (11094)
  hydrogen bonds       : bond        0.03204 (  300)
  hydrogen bonds       : angle       3.69196 (  873)
  Misc. bond           : bond        0.00138 (    1)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: P   84 HIS cc_start: 0.7895 (t-90) cc_final: 0.7646 (t-170)
REVERT: P  293 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6687 (ptp)
REVERT: P  766 MET cc_start: 0.4169 (OUTLIER) cc_final: 0.3124 (ptp)
REVERT: P  861 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7610 (tp30)
REVERT: P  865 GLU cc_start: 0.7700 (tp30) cc_final: 0.7303 (tp30)
REVERT: P  894 SER cc_start: 0.8737 (m) cc_final: 0.8210 (t)
REVERT: P 1006 LEU cc_start: 0.8560 (tt) cc_final: 0.8278 (mm)
REVERT: P 1046 GLU cc_start: 0.7365 (mp0) cc_final: 0.7143 (mp0)
  outliers start: 25
  outliers final: 16
  residues processed: 126
  average time/residue: 0.0810
  time to fit residues: 14.7675
Evaluate side-chains
  125 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  176 ILE
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  293 MET
Chi-restraints excluded: chain P residue  355 THR
Chi-restraints excluded: chain P residue  424 HIS
Chi-restraints excluded: chain P residue  435 LEU
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  551 LEU
Chi-restraints excluded: chain P residue  622 VAL
Chi-restraints excluded: chain P residue  632 SER
Chi-restraints excluded: chain P residue  637 MET
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  735 VAL
Chi-restraints excluded: chain P residue  759 THR
Chi-restraints excluded: chain P residue  766 MET
Chi-restraints excluded: chain P residue  871 TYR
Chi-restraints excluded: chain P residue  903 VAL
Chi-restraints excluded: chain P residue 1091 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 59 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0770
   chunk 24 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.7940

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

Flipped N/Q/H residues before XYZ refinement:
P 491 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.146842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.116852 restraints weight = 16155.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.118939 restraints weight = 10568.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.120287 restraints weight = 7919.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.120789 restraints weight = 6628.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.121703 restraints weight = 6487.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.7163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8140  Z= 0.130
  Angle     :  0.930  30.464  11094  Z= 0.381
  Chirality :  0.043   0.162   1318
  Planarity :  0.005   0.061   1395
  Dihedral  :  5.481 103.960   1125
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 26.77 %
    Favored  : 70.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.27), residues: 1016
  helix:  1.23 (0.29), residues: 404
  sheet: -1.38 (0.60), residues: 74
  loop : -2.78 (0.24), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG P 544 
 TYR   0.009   0.001   TYR P 241 
 PHE   0.015   0.001   PHE P1159 
 TRP   0.021   0.002   TRP P  45 
 HIS   0.002   0.000   HIS P 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8139)
  covalent geometry    : angle       0.92992 (11094)
  hydrogen bonds       : bond        0.03337 (  300)
  hydrogen bonds       : angle       3.69703 (  873)
  Misc. bond           : bond        0.00172 (    1)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: P   84 HIS cc_start: 0.7912 (t-90) cc_final: 0.7635 (t-170)
REVERT: P  293 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.6675 (ptp)
REVERT: P  339 MET cc_start: 0.7544 (mmm) cc_final: 0.7238 (mtt)
REVERT: P  579 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7346 (mp0)
REVERT: P  637 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7378 (tmm)
REVERT: P  766 MET cc_start: 0.4505 (OUTLIER) cc_final: 0.4119 (pmm)
REVERT: P  861 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7578 (tp30)
REVERT: P  865 GLU cc_start: 0.7802 (tp30) cc_final: 0.7396 (tp30)
REVERT: P  894 SER cc_start: 0.8744 (m) cc_final: 0.8251 (t)
REVERT: P 1006 LEU cc_start: 0.8583 (tt) cc_final: 0.8305 (mm)
REVERT: P 1046 GLU cc_start: 0.7465 (mp0) cc_final: 0.7211 (mp0)
  outliers start: 24
  outliers final: 17
  residues processed: 125
  average time/residue: 0.0779
  time to fit residues: 13.9760
Evaluate side-chains
  127 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  176 ILE
Chi-restraints excluded: chain P residue  189 ASP
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  293 MET
Chi-restraints excluded: chain P residue  355 THR
Chi-restraints excluded: chain P residue  424 HIS
Chi-restraints excluded: chain P residue  435 LEU
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  551 LEU
Chi-restraints excluded: chain P residue  579 GLU
Chi-restraints excluded: chain P residue  622 VAL
Chi-restraints excluded: chain P residue  637 MET
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  735 VAL
Chi-restraints excluded: chain P residue  736 ILE
Chi-restraints excluded: chain P residue  759 THR
Chi-restraints excluded: chain P residue  766 MET
Chi-restraints excluded: chain P residue  871 TYR
Chi-restraints excluded: chain P residue  903 VAL
Chi-restraints excluded: chain P residue  954 ILE
Chi-restraints excluded: chain P residue 1091 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0050
   chunk 2 optimal weight:    0.0770
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.5752

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.147630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.117887 restraints weight = 16237.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.119813 restraints weight = 10509.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.121482 restraints weight = 8115.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.121714 restraints weight = 6496.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.121876 restraints weight = 6464.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.7212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8140  Z= 0.118
  Angle     :  0.935  30.107  11094  Z= 0.385
  Chirality :  0.043   0.161   1318
  Planarity :  0.005   0.063   1395
  Dihedral  :  5.486 108.825   1125
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 27.68 %
    Favored  : 70.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.27), residues: 1016
  helix:  1.22 (0.28), residues: 405
  sheet: -1.26 (0.63), residues: 72
  loop : -2.70 (0.24), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P 745 
 TYR   0.009   0.001   TYR P 241 
 PHE   0.015   0.001   PHE P1159 
 TRP   0.051   0.002   TRP P  55 
 HIS   0.001   0.000   HIS P 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8139)
  covalent geometry    : angle       0.93510 (11094)
  hydrogen bonds       : bond        0.03254 (  300)
  hydrogen bonds       : angle       3.65238 (  873)
  Misc. bond           : bond        0.00141 (    1)

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: P   84 HIS cc_start: 0.7873 (t-90) cc_final: 0.7601 (t-170)
REVERT: P  293 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6560 (ptp)
REVERT: P  339 MET cc_start: 0.7528 (mmm) cc_final: 0.7232 (mtt)
REVERT: P  579 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7352 (mp0)
REVERT: P  766 MET cc_start: 0.4417 (OUTLIER) cc_final: 0.4123 (pmm)
REVERT: P  861 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7580 (tp30)
REVERT: P  865 GLU cc_start: 0.7778 (tp30) cc_final: 0.7356 (tp30)
REVERT: P  894 SER cc_start: 0.8706 (m) cc_final: 0.8186 (t)
REVERT: P 1006 LEU cc_start: 0.8594 (tt) cc_final: 0.8253 (mm)
REVERT: P 1046 GLU cc_start: 0.7514 (mp0) cc_final: 0.7261 (mp0)
  outliers start: 20
  outliers final: 12
  residues processed: 124
  average time/residue: 0.0762
  time to fit residues: 13.5531
Evaluate side-chains
  122 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  293 MET
Chi-restraints excluded: chain P residue  355 THR
Chi-restraints excluded: chain P residue  424 HIS
Chi-restraints excluded: chain P residue  435 LEU
Chi-restraints excluded: chain P residue  551 LEU
Chi-restraints excluded: chain P residue  579 GLU
Chi-restraints excluded: chain P residue  622 VAL
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  735 VAL
Chi-restraints excluded: chain P residue  736 ILE
Chi-restraints excluded: chain P residue  759 THR
Chi-restraints excluded: chain P residue  766 MET
Chi-restraints excluded: chain P residue  871 TYR
Chi-restraints excluded: chain P residue  903 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 54 optimal weight:    0.0670
   chunk 64 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.6322

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.147096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.117308 restraints weight = 16262.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.118574 restraints weight = 10858.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.119348 restraints weight = 8793.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.120126 restraints weight = 7651.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.120369 restraints weight = 7126.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.7366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8140  Z= 0.119
  Angle     :  0.945  30.101  11094  Z= 0.387
  Chirality :  0.044   0.185   1318
  Planarity :  0.005   0.060   1395
  Dihedral  :  5.496 115.414   1125
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 28.25 %
    Favored  : 69.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.26 (0.27), residues: 1016
  helix:  1.25 (0.28), residues: 406
  sheet: -1.28 (0.63), residues: 72
  loop : -2.59 (0.24), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P 544 
 TYR   0.009   0.001   TYR P 241 
 PHE   0.014   0.001   PHE P1159 
 TRP   0.042   0.002   TRP P  55 
 HIS   0.001   0.000   HIS P 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8139)
  covalent geometry    : angle       0.94478 (11094)
  hydrogen bonds       : bond        0.03187 (  300)
  hydrogen bonds       : angle       3.63486 (  873)
  Misc. bond           : bond        0.00162 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1420.31 seconds
wall clock time: 25 minutes 20.83 seconds (1520.83 seconds total)