Starting phenix.real_space_refine
on Wed Feb 12 17:58:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ies_35392/02_2025/8ies_35392.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ies_35392/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ies_35392/02_2025/8ies_35392.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ies_35392/02_2025/8ies_35392.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ies_35392/02_2025/8ies_35392.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ies_35392/02_2025/8ies_35392.cif"
  }
  resolution = 3.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.056
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.37, per 1000 atoms: 0.67
  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: 2.19
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.91
  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: 2.34

  Time building geometry restraints manager: 2.50 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.660
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.730
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.470
-------------------------------------------------------------------------------
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   8139  Z= 0.181
  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 : 5.19
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.007   0.000   TRP P  55 
 HIS   0.001   0.000   HIS P  51 
 PHE   0.003   0.000   PHE P1128 
 TYR   0.003   0.000   TYR P 241 
 ARG   0.001   0.000   ARG P 201 

*********************** 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  : 0.857 
Fit side-chains
   revert: symmetry clash
REVERT: P   40 TYR cc_start: 0.4402 (m-80) cc_final: 0.3237 (m-80)
REVERT: P  437 LEU cc_start: 0.8732 (pp) cc_final: 0.8469 (mp)
REVERT: P  641 VAL cc_start: 0.8123 (t) cc_final: 0.7740 (p)
REVERT: P  942 LEU cc_start: 0.9024 (tp) cc_final: 0.8574 (tp)
REVERT: P 1012 VAL cc_start: 0.7641 (t) cc_final: 0.7411 (t)
REVERT: P 1046 GLU cc_start: 0.7213 (mp0) cc_final: 0.6795 (mp0)
REVERT: P 1164 ARG cc_start: 0.8838 (tmm160) cc_final: 0.8636 (ptm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.2655
  time to fit residues: 69.4089
Evaluate side-chains
  118 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 59 optimal weight:    8.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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
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: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.169041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.139373 restraints weight = 16862.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.143032 restraints weight = 10030.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.145483 restraints weight = 7142.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8139  Z= 0.211
  Angle     :  0.934  30.754  11094  Z= 0.380
  Chirality :  0.044   0.243   1318
  Planarity :  0.005   0.033   1395
  Dihedral  :  6.755 136.088   1125
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.03 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.25), residues: 1016
  helix:  0.58 (0.28), residues: 394
  sheet: -2.35 (0.55), residues: 75
  loop : -3.61 (0.21), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP P  55 
 HIS   0.007   0.001   HIS P  84 
 PHE   0.012   0.001   PHE P 512 
 TYR   0.027   0.002   TYR P 241 
 ARG   0.005   0.001   ARG P 627 

*********************** 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
  152 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
REVERT: P  437 LEU cc_start: 0.8707 (pp) cc_final: 0.8411 (mp)
REVERT: P 1046 GLU cc_start: 0.7330 (mp0) cc_final: 0.7070 (mp0)
  outliers start: 15
  outliers final: 10
  residues processed: 146
  average time/residue: 0.2076
  time to fit residues: 41.0964
Evaluate side-chains
  121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  291 LEU
Chi-restraints excluded: chain P residue  408 VAL
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  525 VAL
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 87 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 89 optimal weight:    0.0770
   chunk 94 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.1544

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

Flipped N/Q/H residues before XYZ refinement:
P 101 GLN
P 369 HIS
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 = 0.4205 r_free = 0.4205 target = 0.154690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.123317 restraints weight = 16677.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.125650 restraints weight = 10483.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.126887 restraints weight = 8377.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.4885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8139  Z= 0.263
  Angle     :  0.971  31.727  11094  Z= 0.405
  Chirality :  0.046   0.213   1318
  Planarity :  0.005   0.056   1395
  Dihedral  :  6.596 126.815   1125
  Min Nonbonded Distance : 1.789

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 19.36 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.26), residues: 1016
  helix:  0.80 (0.28), residues: 394
  sheet: -2.55 (0.49), residues: 91
  loop : -3.41 (0.22), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP P  45 
 HIS   0.004   0.001   HIS P  84 
 PHE   0.012   0.002   PHE P 494 
 TYR   0.016   0.002   TYR P 183 
 ARG   0.008   0.001   ARG P 164 

*********************** 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
  157 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
REVERT: P  267 SER cc_start: 0.7869 (m) cc_final: 0.7610 (p)
REVERT: P  437 LEU cc_start: 0.8692 (pp) cc_final: 0.8377 (mp)
REVERT: P  573 MET cc_start: 0.7250 (ttm) cc_final: 0.6643 (ttt)
REVERT: P  854 MET cc_start: 0.8598 (mmp) cc_final: 0.8240 (mmp)
REVERT: P  894 SER cc_start: 0.8897 (m) cc_final: 0.8460 (t)
  outliers start: 26
  outliers final: 15
  residues processed: 151
  average time/residue: 0.1758
  time to fit residues: 37.7628
Evaluate side-chains
  118 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  278 THR
Chi-restraints excluded: chain P residue  318 LEU
Chi-restraints excluded: chain P residue  340 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  634 LEU
Chi-restraints excluded: chain P residue  735 VAL
Chi-restraints excluded: chain P residue  759 THR
Chi-restraints excluded: chain P residue  773 LEU
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  903 VAL
Chi-restraints excluded: chain P residue  954 ILE
Chi-restraints excluded: chain P residue  986 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 98 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0040
   chunk 101 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 58 optimal weight:    0.4980
   chunk 76 optimal weight:    0.0970
   chunk 78 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
P  84 HIS
** P 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 413 HIS
P 485 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.154741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.122580 restraints weight = 16505.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.126131 restraints weight = 10063.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.128462 restraints weight = 7357.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.5216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8139  Z= 0.165
  Angle     :  0.900  30.643  11094  Z= 0.360
  Chirality :  0.043   0.150   1318
  Planarity :  0.004   0.059   1395
  Dihedral  :  6.173 119.264   1125
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 21.64 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.27), residues: 1016
  helix:  1.25 (0.29), residues: 390
  sheet: -2.10 (0.54), residues: 82
  loop : -3.18 (0.23), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP P  55 
 HIS   0.013   0.001   HIS P  84 
 PHE   0.020   0.001   PHE P 494 
 TYR   0.010   0.001   TYR P 241 
 ARG   0.005   0.000   ARG P  76 

*********************** 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
  134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
REVERT: P   76 ARG cc_start: 0.6858 (ttp80) cc_final: 0.6624 (ptm-80)
REVERT: P  293 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6554 (ptp)
REVERT: P  437 LEU cc_start: 0.8672 (pp) cc_final: 0.8382 (mp)
REVERT: P  766 MET cc_start: 0.4025 (OUTLIER) cc_final: 0.3028 (ptp)
REVERT: P  854 MET cc_start: 0.8659 (mmp) cc_final: 0.8310 (mmp)
REVERT: P  861 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7327 (tp30)
REVERT: P  893 ILE cc_start: 0.8972 (mm) cc_final: 0.8273 (mm)
REVERT: P  894 SER cc_start: 0.8792 (m) cc_final: 0.8336 (t)
REVERT: P 1046 GLU cc_start: 0.7318 (mp0) cc_final: 0.6915 (mp0)
  outliers start: 21
  outliers final: 10
  residues processed: 126
  average time/residue: 0.1967
  time to fit residues: 34.8422
Evaluate side-chains
  117 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  293 MET
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  612 LEU
Chi-restraints excluded: chain P residue  634 LEU
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  773 LEU
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  967 ASP
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 6 optimal weight:    0.0980
   chunk 91 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0270
   chunk 34 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
P 485 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.153221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.122587 restraints weight = 16486.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.125508 restraints weight = 11221.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.126626 restraints weight = 7693.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.5518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8139  Z= 0.169
  Angle     :  0.892  30.567  11094  Z= 0.355
  Chirality :  0.042   0.143   1318
  Planarity :  0.004   0.048   1395
  Dihedral  :  5.949 115.444   1125
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 22.10 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.27), residues: 1016
  helix:  1.33 (0.29), residues: 392
  sheet: -1.85 (0.54), residues: 81
  loop : -3.05 (0.23), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP P  45 
 HIS   0.002   0.001   HIS P 836 
 PHE   0.030   0.001   PHE P 243 
 TYR   0.008   0.001   TYR P 940 
 ARG   0.004   0.000   ARG P 279 

*********************** 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
  134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: P  437 LEU cc_start: 0.8713 (pp) cc_final: 0.8366 (mp)
REVERT: P  766 MET cc_start: 0.3861 (pmm) cc_final: 0.2866 (ptp)
REVERT: P  854 MET cc_start: 0.8769 (mmp) cc_final: 0.8477 (mmp)
REVERT: P  861 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7244 (tp30)
REVERT: P  865 GLU cc_start: 0.7447 (tp30) cc_final: 0.6974 (tp30)
REVERT: P  894 SER cc_start: 0.8770 (m) cc_final: 0.8262 (t)
REVERT: P 1046 GLU cc_start: 0.7144 (mp0) cc_final: 0.6668 (mp0)
  outliers start: 24
  outliers final: 16
  residues processed: 130
  average time/residue: 0.1677
  time to fit residues: 31.5644
Evaluate side-chains
  120 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  262 CYS
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  612 LEU
Chi-restraints excluded: chain P residue  634 LEU
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  773 LEU
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 1138 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 30 optimal weight:    0.4980
   chunk 43 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0980
   chunk 78 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 80 optimal weight:    0.3980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
P 753 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.152370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.123888 restraints weight = 16319.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.124222 restraints weight = 10923.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.125398 restraints weight = 9919.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.5789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8139  Z= 0.159
  Angle     :  0.895  30.228  11094  Z= 0.354
  Chirality :  0.042   0.143   1318
  Planarity :  0.004   0.056   1395
  Dihedral  :  5.662 111.877   1125
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 23.35 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.27), residues: 1016
  helix:  1.40 (0.29), residues: 395
  sheet: -1.71 (0.56), residues: 81
  loop : -2.88 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP P  45 
 HIS   0.001   0.000   HIS P 780 
 PHE   0.021   0.001   PHE P 243 
 TYR   0.007   0.001   TYR P 940 
 ARG   0.003   0.000   ARG P 279 

*********************** 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
  132 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  293 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6563 (ptp)
REVERT: P  437 LEU cc_start: 0.8722 (pp) cc_final: 0.8346 (mp)
REVERT: P  766 MET cc_start: 0.3826 (OUTLIER) cc_final: 0.2921 (ptp)
REVERT: P  854 MET cc_start: 0.8768 (mmp) cc_final: 0.8521 (mmp)
REVERT: P  861 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7408 (tp30)
  outliers start: 29
  outliers final: 15
  residues processed: 121
  average time/residue: 0.1786
  time to fit residues: 31.0357
Evaluate side-chains
  114 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
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  318 LEU
Chi-restraints excluded: chain P residue  334 VAL
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  612 LEU
Chi-restraints excluded: chain P residue  634 LEU
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  773 LEU
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  903 VAL
Chi-restraints excluded: chain P residue  978 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 96 optimal weight:    0.5980
   chunk 10 optimal weight:    5.9990
   chunk 40 optimal weight:    0.3980
   chunk 6 optimal weight:    3.9990
   chunk 35 optimal weight:    0.4980
   chunk 54 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0770
   chunk 74 optimal weight:    0.0050
   chunk 66 optimal weight:    0.1980
   overall best weight:    0.2352

-------------------------------------------------------------------------------
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 = 0.4191 r_free = 0.4191 target = 0.153328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.123883 restraints weight = 16440.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.125088 restraints weight = 11750.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.126988 restraints weight = 9030.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.5846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8139  Z= 0.146
  Angle     :  0.895  29.909  11094  Z= 0.355
  Chirality :  0.042   0.148   1318
  Planarity :  0.004   0.047   1395
  Dihedral  :  5.488 111.210   1125
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 23.58 %
    Favored  : 73.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.27), residues: 1016
  helix:  1.41 (0.29), residues: 396
  sheet: -1.13 (0.62), residues: 71
  loop : -2.78 (0.24), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP P  45 
 HIS   0.002   0.000   HIS P 822 
 PHE   0.021   0.001   PHE P 243 
 TYR   0.029   0.001   TYR P 183 
 ARG   0.004   0.000   ARG P 740 

*********************** 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
  120 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  271 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7638 (mt)
REVERT: P  437 LEU cc_start: 0.8716 (pp) cc_final: 0.8342 (mp)
REVERT: P  766 MET cc_start: 0.4164 (OUTLIER) cc_final: 0.2942 (ptp)
REVERT: P  854 MET cc_start: 0.8773 (mmp) cc_final: 0.8533 (mmp)
REVERT: P  861 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7398 (tp30)
REVERT: P  893 ILE cc_start: 0.8712 (mm) cc_final: 0.8449 (mm)
  outliers start: 22
  outliers final: 11
  residues processed: 112
  average time/residue: 0.1946
  time to fit residues: 31.1085
Evaluate side-chains
  109 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  271 ILE
Chi-restraints excluded: chain P residue  334 VAL
Chi-restraints excluded: chain P residue  355 THR
Chi-restraints excluded: chain P residue  424 HIS
Chi-restraints excluded: chain P residue  551 LEU
Chi-restraints excluded: chain P residue  612 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  766 MET
Chi-restraints excluded: chain P residue  773 LEU
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 92 optimal weight:    0.0070
   chunk 96 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 47 optimal weight:    0.2980
   chunk 32 optimal weight:    0.5980
   chunk 97 optimal weight:    0.5980
   chunk 7 optimal weight:    0.2980
   chunk 28 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0050
   overall best weight:    0.2412

-------------------------------------------------------------------------------
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 = 0.4192 r_free = 0.4192 target = 0.153533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.122556 restraints weight = 16315.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.125735 restraints weight = 10000.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.127526 restraints weight = 7549.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.5923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8139  Z= 0.150
  Angle     :  0.892  29.920  11094  Z= 0.355
  Chirality :  0.043   0.182   1318
  Planarity :  0.004   0.048   1395
  Dihedral  :  5.418 112.618   1125
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 23.69 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.27), residues: 1016
  helix:  1.46 (0.29), residues: 395
  sheet: -1.01 (0.63), residues: 71
  loop : -2.69 (0.24), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP P  45 
 HIS   0.003   0.000   HIS P 822 
 PHE   0.019   0.001   PHE P 243 
 TYR   0.023   0.001   TYR P 183 
 ARG   0.014   0.000   ARG P 740 

*********************** 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
  123 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   40 TYR cc_start: 0.5393 (OUTLIER) cc_final: 0.3759 (m-80)
REVERT: P  271 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7661 (mt)
REVERT: P  437 LEU cc_start: 0.8686 (pp) cc_final: 0.8363 (mp)
REVERT: P  854 MET cc_start: 0.8849 (mmp) cc_final: 0.8613 (mmp)
REVERT: P  861 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7399 (tp30)
REVERT: P  893 ILE cc_start: 0.8867 (mm) cc_final: 0.8578 (mm)
  outliers start: 23
  outliers final: 17
  residues processed: 115
  average time/residue: 0.1810
  time to fit residues: 29.8013
Evaluate side-chains
  114 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   40 TYR
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  271 ILE
Chi-restraints excluded: chain P residue  334 VAL
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  612 LEU
Chi-restraints excluded: chain P residue  634 LEU
Chi-restraints excluded: chain P residue  637 MET
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  773 LEU
Chi-restraints excluded: chain P residue  903 VAL
Chi-restraints excluded: chain P residue  956 THR
Chi-restraints excluded: chain P residue  978 MET
Chi-restraints excluded: chain P residue 1138 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0980
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0370
   chunk 59 optimal weight:    0.9980
   chunk 2 optimal weight:   10.0000
   overall best weight:    0.4658

-------------------------------------------------------------------------------
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 = 0.4171 r_free = 0.4171 target = 0.151835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.122233 restraints weight = 16653.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.124176 restraints weight = 11630.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.125645 restraints weight = 8464.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.6163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8139  Z= 0.165
  Angle     :  0.918  30.188  11094  Z= 0.369
  Chirality :  0.043   0.215   1318
  Planarity :  0.004   0.051   1395
  Dihedral  :  5.365 116.550   1125
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 23.92 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.27), residues: 1016
  helix:  1.44 (0.29), residues: 395
  sheet: -0.93 (0.63), residues: 71
  loop : -2.64 (0.24), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP P  45 
 HIS   0.002   0.000   HIS P 190 
 PHE   0.018   0.001   PHE P 243 
 TYR   0.020   0.001   TYR P 183 
 ARG   0.008   0.000   ARG P 740 

*********************** 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
  120 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: P   40 TYR cc_start: 0.5079 (OUTLIER) cc_final: 0.3471 (m-80)
REVERT: P  271 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7563 (mt)
REVERT: P  766 MET cc_start: 0.4683 (pmm) cc_final: 0.4096 (pmm)
REVERT: P  854 MET cc_start: 0.8823 (mmp) cc_final: 0.8603 (mmp)
REVERT: P  861 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7456 (tp30)
  outliers start: 22
  outliers final: 18
  residues processed: 113
  average time/residue: 0.1925
  time to fit residues: 30.8071
Evaluate side-chains
  117 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   40 TYR
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  271 ILE
Chi-restraints excluded: chain P residue  334 VAL
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  612 LEU
Chi-restraints excluded: chain P residue  634 LEU
Chi-restraints excluded: chain P residue  637 MET
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  773 LEU
Chi-restraints excluded: chain P residue  903 VAL
Chi-restraints excluded: chain P residue  956 THR
Chi-restraints excluded: chain P residue  978 MET
Chi-restraints excluded: chain P residue 1138 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0770
   chunk 47 optimal weight:    0.0010
   chunk 2 optimal weight:    0.2980
   chunk 17 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.3944

-------------------------------------------------------------------------------
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**
P 491 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.151957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.120982 restraints weight = 16325.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.124476 restraints weight = 10347.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.125781 restraints weight = 7413.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.6281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8139  Z= 0.156
  Angle     :  0.920  30.091  11094  Z= 0.371
  Chirality :  0.043   0.248   1318
  Planarity :  0.004   0.055   1395
  Dihedral  :  5.372 119.783   1125
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 24.83 %
    Favored  : 72.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.27), residues: 1016
  helix:  1.49 (0.29), residues: 396
  sheet: -0.77 (0.64), residues: 71
  loop : -2.55 (0.24), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP P  45 
 HIS   0.002   0.000   HIS P 822 
 PHE   0.018   0.001   PHE P 243 
 TYR   0.011   0.001   TYR P 183 
 ARG   0.009   0.000   ARG P 740 

********************** 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
  122 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
REVERT: P   40 TYR cc_start: 0.5268 (OUTLIER) cc_final: 0.3739 (m-80)
REVERT: P   84 HIS cc_start: 0.7644 (t-90) cc_final: 0.7440 (t-170)
REVERT: P  271 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7559 (mt)
REVERT: P  437 LEU cc_start: 0.8785 (pp) cc_final: 0.8481 (mp)
REVERT: P  766 MET cc_start: 0.3878 (pmm) cc_final: 0.2079 (ptp)
REVERT: P  861 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7430 (tp30)
REVERT: P 1034 ARG cc_start: 0.6492 (mmm160) cc_final: 0.6276 (mmm160)
  outliers start: 20
  outliers final: 16
  residues processed: 115
  average time/residue: 0.1900
  time to fit residues: 30.9488
Evaluate side-chains
  115 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   40 TYR
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  271 ILE
Chi-restraints excluded: chain P residue  334 VAL
Chi-restraints excluded: chain P residue  355 THR
Chi-restraints excluded: chain P residue  424 HIS
Chi-restraints excluded: chain P residue  551 LEU
Chi-restraints excluded: chain P residue  612 LEU
Chi-restraints excluded: chain P residue  634 LEU
Chi-restraints excluded: chain P residue  637 MET
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  773 LEU
Chi-restraints excluded: chain P residue  903 VAL
Chi-restraints excluded: chain P residue  956 THR
Chi-restraints excluded: chain P residue 1138 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0980
   chunk 23 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 54 optimal weight:    0.2980
   chunk 42 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    0.5982

-------------------------------------------------------------------------------
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 = 0.4143 r_free = 0.4143 target = 0.149419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.119204 restraints weight = 16265.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.121223 restraints weight = 11101.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.121962 restraints weight = 8386.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.6632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8139  Z= 0.179
  Angle     :  0.933  30.168  11094  Z= 0.377
  Chirality :  0.044   0.266   1318
  Planarity :  0.004   0.053   1395
  Dihedral  :  5.463 126.953   1125
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 25.17 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.27), residues: 1016
  helix:  1.48 (0.29), residues: 397
  sheet: -0.69 (0.64), residues: 71
  loop : -2.51 (0.25), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP P  45 
 HIS   0.002   0.000   HIS P 822 
 PHE   0.021   0.001   PHE P 445 
 TYR   0.010   0.001   TYR P 183 
 ARG   0.008   0.000   ARG P 740 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2502.91 seconds
wall clock time: 45 minutes 48.36 seconds (2748.36 seconds total)