Starting phenix.real_space_refine
on Fri Nov 15 03:38:15 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ies_35392/11_2024/8ies_35392.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ies_35392/11_2024/8ies_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ies_35392/11_2024/8ies_35392.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ies_35392/11_2024/8ies_35392.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ies_35392/11_2024/8ies_35392.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ies_35392/11_2024/8ies_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-5513/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: 5.10, per 1000 atoms: 0.64
  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: 2.16
  Conformation dependent library (CDL) restraints added in 942.9 milliseconds
  

  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: 0.88
  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: 2.42 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:             1.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.940
  Find NCS groups from input model:        0.070
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.320
-------------------------------------------------------------------------------
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  : 0.911 
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: 0.2639
  time to fit residues: 68.9401
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  : 0.968 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
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  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: P  437 LEU cc_start: 0.8685 (pp) cc_final: 0.8412 (mp)
REVERT: P 1046 GLU cc_start: 0.7446 (mp0) cc_final: 0.7071 (mp0)
  outliers start: 15
  outliers final: 10
  residues processed: 146
  average time/residue: 0.2140
  time to fit residues: 42.5597
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  : 0.882 
-------------------------------------------------------------------------------
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 51 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 92 optimal weight:    0.5980
   chunk 100 optimal weight:    0.0980
   chunk 82 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
P 101 GLN
P 897 GLN
P1057 GLN
P1127 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.3752

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= 0.168
  Angle     :  0.894  30.335  11094  Z= 0.356
  Chirality :  0.043   0.176   1318
  Planarity :  0.004   0.054   1395
  Dihedral  :  6.415 135.176   1125
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 17.88 %
    Favored  : 80.18 %
  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: -2.09 (0.26), residues: 1016
  helix:  1.11 (0.29), residues: 388
  sheet: -1.84 (0.58), residues: 75
  loop : -3.42 (0.22), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP P  45 
 HIS   0.002   0.001   HIS P  84 
 PHE   0.009   0.001   PHE P 246 
 TYR   0.013   0.001   TYR P 183 
 ARG   0.007   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
  139 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.909 
Fit side-chains
REVERT: P  437 LEU cc_start: 0.8701 (pp) cc_final: 0.8419 (mp)
REVERT: P  893 ILE cc_start: 0.8426 (mm) cc_final: 0.7820 (mm)
REVERT: P 1046 GLU cc_start: 0.7474 (mp0) cc_final: 0.7117 (mp0)
  outliers start: 17
  outliers final: 6
  residues processed: 133
  average time/residue: 0.1775
  time to fit residues: 33.8502
Evaluate side-chains
  111 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  373 THR
Chi-restraints excluded: chain P residue  424 HIS
Chi-restraints excluded: chain P residue  464 LEU
Chi-restraints excluded: chain P residue  735 VAL
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 69 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 44 optimal weight:    0.3980
   chunk 62 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 98 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0070
   overall best weight:    0.7600

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

Flipped N/Q/H residues before XYZ refinement:
P 413 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.4689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8139  Z= 0.197
  Angle     :  0.911  31.081  11094  Z= 0.365
  Chirality :  0.043   0.147   1318
  Planarity :  0.004   0.065   1395
  Dihedral  :  6.192 118.687   1125
  Min Nonbonded Distance : 1.870

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.07 %
    Favored  : 76.77 %
  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: -1.88 (0.27), residues: 1016
  helix:  1.18 (0.29), residues: 396
  sheet: -1.89 (0.55), residues: 81
  loop : -3.24 (0.23), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP P  45 
 HIS   0.004   0.001   HIS P 559 
 PHE   0.017   0.001   PHE P1056 
 TYR   0.020   0.001   TYR P 183 
 ARG   0.009   0.001   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
  135 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.960 
Fit side-chains
REVERT: P   76 ARG cc_start: 0.7166 (ttp80) cc_final: 0.6963 (ptm-80)
REVERT: P  267 SER cc_start: 0.7947 (m) cc_final: 0.7686 (p)
REVERT: P  293 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6741 (ptp)
REVERT: P  437 LEU cc_start: 0.8663 (pp) cc_final: 0.8349 (mp)
REVERT: P  498 PRO cc_start: 0.7963 (Cg_endo) cc_final: 0.7759 (Cg_exo)
REVERT: P  893 ILE cc_start: 0.8757 (mm) cc_final: 0.8499 (mm)
REVERT: P 1046 GLU cc_start: 0.7391 (mp0) cc_final: 0.7100 (mp0)
  outliers start: 19
  outliers final: 12
  residues processed: 130
  average time/residue: 0.1750
  time to fit residues: 32.7171
Evaluate side-chains
  112 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  271 ILE
Chi-restraints excluded: chain P residue  293 MET
Chi-restraints excluded: chain P residue  318 LEU
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  773 LEU
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 1 optimal weight:   20.0000
   chunk 73 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 88 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
P  81 ASN
P  84 HIS
P 369 HIS
P 753 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.6757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   8139  Z= 0.398
  Angle     :  1.058  33.576  11094  Z= 0.459
  Chirality :  0.049   0.155   1318
  Planarity :  0.006   0.089   1395
  Dihedral  :  6.614 105.505   1125
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 22.32 %
    Favored  : 73.46 %
  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: -2.18 (0.26), residues: 1016
  helix:  0.64 (0.27), residues: 403
  sheet: -2.17 (0.54), residues: 83
  loop : -3.18 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP P  45 
 HIS   0.014   0.002   HIS P  84 
 PHE   0.018   0.002   PHE P1021 
 TYR   0.013   0.002   TYR P 276 
 ARG   0.008   0.001   ARG P1158 

*********************** 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
  145 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 108
  time to evaluate  : 0.925 
Fit side-chains
REVERT: P  243 PHE cc_start: 0.8572 (t80) cc_final: 0.8303 (t80)
REVERT: P  267 SER cc_start: 0.8228 (m) cc_final: 0.8003 (p)
REVERT: P  279 ARG cc_start: 0.7029 (ttm-80) cc_final: 0.6791 (ptm160)
REVERT: P  293 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7121 (ptp)
REVERT: P  766 MET cc_start: 0.4642 (OUTLIER) cc_final: 0.3965 (ptp)
REVERT: P  894 SER cc_start: 0.9080 (m) cc_final: 0.8592 (t)
REVERT: P 1046 GLU cc_start: 0.7462 (mp0) cc_final: 0.7162 (mp0)
  outliers start: 37
  outliers final: 24
  residues processed: 134
  average time/residue: 0.1738
  time to fit residues: 33.1663
Evaluate side-chains
  124 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
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  293 MET
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  458 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  634 LEU
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  669 VAL
Chi-restraints excluded: chain P residue  687 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  873 VAL
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  986 VAL
Chi-restraints excluded: chain P residue 1029 PHE
Chi-restraints excluded: chain P residue 1049 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 57 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 32 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   chunk 95 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.6980

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.6753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8139  Z= 0.191
  Angle     :  0.922  30.191  11094  Z= 0.374
  Chirality :  0.044   0.158   1318
  Planarity :  0.005   0.077   1395
  Dihedral  :  5.844  92.961   1125
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 24.49 %
    Favored  : 72.89 %
  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: -1.72 (0.27), residues: 1016
  helix:  1.17 (0.28), residues: 398
  sheet: -2.03 (0.56), residues: 78
  loop : -2.99 (0.23), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP P  45 
 HIS   0.002   0.001   HIS P 772 
 PHE   0.007   0.001   PHE P 103 
 TYR   0.009   0.001   TYR P 183 
 ARG   0.007   0.000   ARG P 989 

*********************** 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
  134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: P  210 MET cc_start: 0.3227 (ptm) cc_final: 0.3005 (ptm)
REVERT: P  279 ARG cc_start: 0.6865 (ttm-80) cc_final: 0.6615 (ptm160)
REVERT: P  293 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6837 (ptp)
REVERT: P  894 SER cc_start: 0.8969 (m) cc_final: 0.8447 (t)
REVERT: P 1046 GLU cc_start: 0.7461 (mp0) cc_final: 0.7242 (mp0)
  outliers start: 23
  outliers final: 16
  residues processed: 126
  average time/residue: 0.1997
  time to fit residues: 34.9336
Evaluate side-chains
  119 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 1.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   40 TYR
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  297 VAL
Chi-restraints excluded: chain P residue  340 VAL
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  653 VAL
Chi-restraints excluded: chain P residue  735 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
Chi-restraints excluded: chain P residue 1149 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 98 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 59 optimal weight:    0.1980
   chunk 45 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 39 optimal weight:    0.5980
   chunk 58 optimal weight:    0.3980
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
P 219 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.6869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8139  Z= 0.177
  Angle     :  0.924  30.266  11094  Z= 0.373
  Chirality :  0.043   0.142   1318
  Planarity :  0.005   0.077   1395
  Dihedral  :  5.565  95.370   1125
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 25.63 %
    Favored  : 72.21 %
  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: -1.50 (0.27), residues: 1016
  helix:  1.35 (0.29), residues: 398
  sheet: -1.61 (0.59), residues: 72
  loop : -2.92 (0.24), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP P  45 
 HIS   0.002   0.001   HIS P 390 
 PHE   0.008   0.001   PHE P 264 
 TYR   0.020   0.001   TYR P 183 
 ARG   0.010   0.001   ARG P  76 

*********************** 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
  130 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: P   76 ARG cc_start: 0.7085 (ttp80) cc_final: 0.6805 (ptm-80)
REVERT: P  279 ARG cc_start: 0.6879 (ttm-80) cc_final: 0.6618 (ptm160)
REVERT: P  766 MET cc_start: 0.4432 (OUTLIER) cc_final: 0.3972 (pmm)
REVERT: P  894 SER cc_start: 0.8804 (m) cc_final: 0.8291 (t)
REVERT: P 1046 GLU cc_start: 0.7444 (mp0) cc_final: 0.7227 (mp0)
  outliers start: 19
  outliers final: 14
  residues processed: 124
  average time/residue: 0.1988
  time to fit residues: 34.1696
Evaluate side-chains
  121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   40 TYR
Chi-restraints excluded: chain P residue  176 ILE
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  297 VAL
Chi-restraints excluded: chain P residue  355 THR
Chi-restraints excluded: chain P residue  424 HIS
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  766 MET
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 1091 VAL
Chi-restraints excluded: chain P residue 1149 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 89 optimal weight:    0.2980
   chunk 94 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.7025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8139  Z= 0.175
  Angle     :  0.924  30.159  11094  Z= 0.376
  Chirality :  0.043   0.143   1318
  Planarity :  0.005   0.073   1395
  Dihedral  :  5.460  96.322   1125
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 26.99 %
    Favored  : 71.18 %
  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: -1.38 (0.27), residues: 1016
  helix:  1.40 (0.29), residues: 399
  sheet: -1.46 (0.60), residues: 72
  loop : -2.82 (0.24), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP P  45 
 HIS   0.002   0.001   HIS P 190 
 PHE   0.019   0.001   PHE P1159 
 TYR   0.018   0.001   TYR P 183 
 ARG   0.007   0.000   ARG P  76 

*********************** 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
  122 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  279 ARG cc_start: 0.6880 (ttm-80) cc_final: 0.6628 (ptm160)
REVERT: P  766 MET cc_start: 0.4399 (OUTLIER) cc_final: 0.3955 (pmm)
REVERT: P  894 SER cc_start: 0.8757 (m) cc_final: 0.8234 (t)
REVERT: P 1046 GLU cc_start: 0.7450 (mp0) cc_final: 0.7244 (mp0)
  outliers start: 16
  outliers final: 14
  residues processed: 117
  average time/residue: 0.1965
  time to fit residues: 31.8468
Evaluate side-chains
  120 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   40 TYR
Chi-restraints excluded: chain P residue  176 ILE
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  297 VAL
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  637 MET
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  735 VAL
Chi-restraints excluded: chain P residue  766 MET
Chi-restraints excluded: chain P residue  903 VAL
Chi-restraints excluded: chain P residue  933 VAL
Chi-restraints excluded: chain P residue  978 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 96 optimal weight:    0.8980
   chunk 59 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.7592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8139  Z= 0.300
  Angle     :  0.990  30.915  11094  Z= 0.418
  Chirality :  0.046   0.152   1318
  Planarity :  0.005   0.072   1395
  Dihedral  :  5.775 107.717   1125
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.04 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 26.65 %
    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 (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:  1.32 (0.28), residues: 395
  sheet: -1.71 (0.58), residues: 78
  loop : -2.79 (0.24), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP P  45 
 HIS   0.004   0.001   HIS P 190 
 PHE   0.017   0.002   PHE P1159 
 TYR   0.013   0.002   TYR P 183 
 ARG   0.006   0.001   ARG P  76 

*********************** 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
  131 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  279 ARG cc_start: 0.6999 (ttm-80) cc_final: 0.6768 (ptm160)
REVERT: P  766 MET cc_start: 0.4847 (OUTLIER) cc_final: 0.4008 (ptp)
REVERT: P  894 SER cc_start: 0.8999 (m) cc_final: 0.8527 (t)
REVERT: P 1006 LEU cc_start: 0.8667 (tt) cc_final: 0.8343 (mm)
REVERT: P 1046 GLU cc_start: 0.7550 (mp0) cc_final: 0.7325 (mp0)
  outliers start: 20
  outliers final: 15
  residues processed: 126
  average time/residue: 0.2016
  time to fit residues: 35.3683
Evaluate side-chains
  121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   40 TYR
Chi-restraints excluded: chain P residue  176 ILE
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  297 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  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  903 VAL
Chi-restraints excluded: chain P residue  933 VAL
Chi-restraints excluded: chain P residue  978 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 93 optimal weight:    0.4980
   chunk 80 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   chunk 11 optimal weight:    7.9990
   overall best weight:    0.7380

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.7618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8139  Z= 0.196
  Angle     :  0.954  29.967  11094  Z= 0.396
  Chirality :  0.044   0.158   1318
  Planarity :  0.005   0.078   1395
  Dihedral  :  5.655 112.658   1125
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 27.68 %
    Favored  : 70.62 %
  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: -1.23 (0.27), residues: 1016
  helix:  1.40 (0.28), residues: 401
  sheet: -1.30 (0.62), residues: 71
  loop : -2.65 (0.24), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP P  45 
 HIS   0.002   0.000   HIS P 626 
 PHE   0.015   0.001   PHE P1159 
 TYR   0.016   0.001   TYR P 183 
 ARG   0.006   0.000   ARG P 989 

********************** 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
  126 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  279 ARG cc_start: 0.6918 (ttm-80) cc_final: 0.6676 (ptm160)
REVERT: P  766 MET cc_start: 0.4710 (OUTLIER) cc_final: 0.3957 (ptp)
REVERT: P  894 SER cc_start: 0.8872 (m) cc_final: 0.8379 (t)
REVERT: P 1006 LEU cc_start: 0.8626 (tt) cc_final: 0.8285 (mm)
  outliers start: 15
  outliers final: 13
  residues processed: 120
  average time/residue: 0.1986
  time to fit residues: 33.1224
Evaluate side-chains
  120 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   40 TYR
Chi-restraints excluded: chain P residue  176 ILE
Chi-restraints excluded: chain P residue  262 CYS
Chi-restraints excluded: chain P residue  297 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  637 MET
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  735 VAL
Chi-restraints excluded: chain P residue  766 MET
Chi-restraints excluded: chain P residue  903 VAL
Chi-restraints excluded: chain P residue  933 VAL
Chi-restraints excluded: chain P residue  978 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 81 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0770
   chunk 71 optimal weight:    0.7980
   chunk 4 optimal weight:    9.9990
   chunk 58 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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 = 0.4074 r_free = 0.4074 target = 0.144228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.114564 restraints weight = 16221.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.114835 restraints weight = 10841.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.116025 restraints weight = 9515.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.7677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8139  Z= 0.185
  Angle     :  0.952  29.895  11094  Z= 0.397
  Chirality :  0.044   0.185   1318
  Planarity :  0.005   0.072   1395
  Dihedral  :  5.622 116.635   1125
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 28.25 %
    Favored  : 70.16 %
  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: -1.20 (0.27), residues: 1016
  helix:  1.30 (0.28), residues: 407
  sheet: -1.21 (0.62), residues: 71
  loop : -2.58 (0.25), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP P 251 
 HIS   0.004   0.001   HIS P 559 
 PHE   0.016   0.001   PHE P1159 
 TYR   0.016   0.001   TYR P 183 
 ARG   0.006   0.000   ARG P 989 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1782.60 seconds
wall clock time: 33 minutes 19.76 seconds (1999.76 seconds total)