Starting phenix.real_space_refine
on Sat Aug 23 05:06:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wf8_37486/08_2025/8wf8_37486.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wf8_37486/08_2025/8wf8_37486.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wf8_37486/08_2025/8wf8_37486.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wf8_37486/08_2025/8wf8_37486.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wf8_37486/08_2025/8wf8_37486.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wf8_37486/08_2025/8wf8_37486.cif"
  }
  resolution = 2.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.113
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: 6
    Type Number    sf(0)   Gaussians
     P      55      5.49       5
     Mg      1      5.21       5
     S      44      5.16       5
     C    6107      2.51       5
     N    1723      2.21       5
     O    2025      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9955
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 8785
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1066, 8763
          Classifications: {'peptide': 1066}
          Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 1033}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 1066, 8763
          Classifications: {'peptide': 1066}
          Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 1033}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 8901
    Chain: "B"
      Number of atoms: 1169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 1169
          Classifications: {'RNA': 55}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 10, 'rna3p_pur': 23, 'rna3p_pyr': 18}
          Link IDs: {'rna2p': 14, 'rna3p': 40}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG A  78 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  78 " occ=0.50
    residue:
      pdb=" N  APHE A1003 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A1003 " occ=0.50
  Time building chain proxies: 3.08, per 1000 atoms: 0.31
  Number of scatterers: 9955
  At special positions: 0
  Unit cell: (87.15, 91.3, 126.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      44     16.00
     P      55     15.00
     Mg      1     11.99
     O    2025      8.00
     N    1723      7.00
     C    6107      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=0, symmetry=0
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 608.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2038

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 7 sheets defined
      63.3% alpha, 8.9% beta
      15 base pairs and 25 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 10
    Processing helix  chain 'A' and resid 10 through 37
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.512A  pdb=" N   LEU A  58 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 83
    Processing helix  chain 'A' and resid 84 through 102
      removed outlier: 4.474A  pdb=" N   ILE A  88 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 132
    Processing helix  chain 'A' and resid 138 through 142
    Processing helix  chain 'A' and resid 145 through 151
    Processing helix  chain 'A' and resid 151 through 175
      removed outlier: 3.610A  pdb=" N   VAL A 165 " --> pdb=" O   ASN A 161 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ASN A 171 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLU A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 186
      removed outlier: 4.856A  pdb=" N   PHE A 183 " --> pdb=" O   GLU A 179 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   ILE A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 236
      removed outlier: 4.002A  pdb=" N   PHE A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 247
    Processing helix  chain 'A' and resid 259 through 269
    Processing helix  chain 'A' and resid 286 through 299
    Processing helix  chain 'A' and resid 302 through 307
    Processing helix  chain 'A' and resid 310 through 316
    Processing helix  chain 'A' and resid 335 through 348
    Processing helix  chain 'A' and resid 391 through 400
      removed outlier: 3.803A  pdb=" N   LYS A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 429
    Processing helix  chain 'A' and resid 482 through 494
    Processing helix  chain 'A' and resid 494 through 518
    Processing helix  chain 'A' and resid 525 through 530
    Processing helix  chain 'A' and resid 532 through 536
    Processing helix  chain 'A' and resid 537 through 546
    Processing helix  chain 'A' and resid 552 through 583
    Processing helix  chain 'A' and resid 598 through 613
    Processing helix  chain 'A' and resid 617 through 621
    Processing helix  chain 'A' and resid 625 through 638
    Processing helix  chain 'A' and resid 644 through 658
      removed outlier: 4.060A  pdb=" N   PHE A 655 " --> pdb=" O   PHE A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 676
      removed outlier: 3.826A  pdb=" N   VAL A 675 " --> pdb=" O   PHE A 671 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE A 676 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 671 through 676'
    Processing helix  chain 'A' and resid 683 through 708
    Processing helix  chain 'A' and resid 721 through 725
    Processing helix  chain 'A' and resid 728 through 739
    Processing helix  chain 'A' and resid 749 through 759
    Processing helix  chain 'A' and resid 760 through 764
    Processing helix  chain 'A' and resid 767 through 771
      removed outlier: 4.088A  pdb=" N   ALA A 771 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 784
      removed outlier: 3.533A  pdb=" N   ALA A 778 " --> pdb=" O   THR A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 794
    Processing helix  chain 'A' and resid 799 through 807
    Processing helix  chain 'A' and resid 821 through 831
    Processing helix  chain 'A' and resid 831 through 850
    Processing helix  chain 'A' and resid 858 through 903
      removed outlier: 3.717A  pdb=" N   VAL A 888 " --> pdb=" O   ARG A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 917
    Processing helix  chain 'A' and resid 924 through 927
    Processing helix  chain 'A' and resid 953 through 955
      No H-bonds generated for 'chain 'A' and resid 953 through 955'
    Processing helix  chain 'A' and resid 956 through 963
    Processing helix  chain 'A' and resid 966 through 975
    Processing helix  chain 'A' and resid 981 through 1013
      Proline residue:  A 996  - end of helix
    Processing helix  chain 'A' and resid 1013 through 1022
      removed outlier: 4.126A  pdb=" N   SER A1017 " --> pdb=" O   TYR A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1027 through 1038
    Processing helix  chain 'A' and resid 1042 through 1058
    Processing helix  chain 'A' and resid 1074 through 1087
    Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 190
    Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 213
    Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 283
      removed outlier: 5.836A  pdb=" N   MET A 930 " --> pdb=" O   GLY A 949 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   GLY A 949 " --> pdb=" O   MET A 930 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 318 through 320
    Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 389
      removed outlier: 6.722A  pdb=" N   ARG A 378 " --> pdb=" O   LYS A 367 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   LYS A 367 " --> pdb=" O   ARG A 378 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   ARG A 380 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   LEU A 365 " --> pdb=" O   ARG A 380 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ILE A 382 " --> pdb=" O   ARG A 363 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   ARG A 363 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   GLN A 384 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LYS A 361 " --> pdb=" O   GLN A 384 " (cutoff:3.500A)
      removed outlier: 5.660A  pdb=" N   LEU A 386 " --> pdb=" O   MET A 359 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 413 through 414
      removed outlier: 4.062A  pdb=" N   LYS A 361 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   GLU A 447 " --> pdb=" O   HIS A 356 " (cutoff:3.500A)
      removed outlier: 11.467A  pdb=" N   ASN A 358 " --> pdb=" O   LYS A 445 " (cutoff:3.500A)
      removed outlier: 16.074A  pdb=" N   LYS A 445 " --> pdb=" O   ASN A 358 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 462 through 464
      removed outlier: 3.751A  pdb=" N   VAL A 462 " --> pdb=" O   VAL A 470 " (cutoff:3.500A)

    499 hydrogen bonds defined for protein.
    1409 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      38 hydrogen bonds
      64 hydrogen bond angles
      0 basepair planarities
      15 basepair parallelities
      25 stacking parallelities
  Total time for adding SS restraints: 2.01

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2051
        1.33 -     1.45: 2938
        1.45 -     1.57: 5077
        1.57 -     1.69: 107
        1.69 -     1.82: 81
  Bond restraints: 10254
  Sorted by residual:
  bond pdb=" CA  ALA A 485 "
       pdb=" CB  ALA A 485 "
    ideal  model  delta    sigma   weight residual
    1.528  1.459  0.069 1.66e-02 3.63e+03 1.73e+01
  bond pdb=" NE  ARG A 885 "
       pdb=" CZ  ARG A 885 "
    ideal  model  delta    sigma   weight residual
    1.326  1.287  0.039 1.10e-02 8.26e+03 1.25e+01
  bond pdb=" O5'   A B  29 "
       pdb=" C5'   A B  29 "
    ideal  model  delta    sigma   weight residual
    1.424  1.472 -0.048 1.50e-02 4.44e+03 1.01e+01
  bond pdb=" CA  SER A 933 "
       pdb=" CB  SER A 933 "
    ideal  model  delta    sigma   weight residual
    1.531  1.474  0.057 1.83e-02 2.99e+03 9.80e+00
  bond pdb=" CA  ALA A 778 "
       pdb=" CB  ALA A 778 "
    ideal  model  delta    sigma   weight residual
    1.528  1.480  0.049 1.56e-02 4.11e+03 9.70e+00
  ... (remaining 10249 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 12773
        2.88 -     5.76: 1138
        5.76 -     8.63: 117
        8.63 -    11.51: 10
       11.51 -    14.39: 3
  Bond angle restraints: 14041
  Sorted by residual:
  angle pdb=" O3'   U B  30 "
        pdb=" P     U B  31 "
        pdb=" O5'   U B  31 "
      ideal   model   delta    sigma   weight residual
     104.00   89.61   14.39 1.50e+00 4.44e-01 9.20e+01
  angle pdb=" N   GLU A 743 "
        pdb=" CA  GLU A 743 "
        pdb=" CB  GLU A 743 "
      ideal   model   delta    sigma   weight residual
     110.21  121.44  -11.23 1.59e+00 3.96e-01 4.99e+01
  angle pdb=" CB  GLU A 743 "
        pdb=" CG  GLU A 743 "
        pdb=" CD  GLU A 743 "
      ideal   model   delta    sigma   weight residual
     112.60  124.34  -11.74 1.70e+00 3.46e-01 4.77e+01
  angle pdb=" C   ASP A 322 "
        pdb=" CA  ASP A 322 "
        pdb=" CB  ASP A 322 "
      ideal   model   delta    sigma   weight residual
     110.79   99.50   11.29 1.66e+00 3.63e-01 4.62e+01
  angle pdb=" CA BPHE A1003 "
        pdb=" CB BPHE A1003 "
        pdb=" CG BPHE A1003 "
      ideal   model   delta    sigma   weight residual
     113.80  120.06   -6.26 1.00e+00 1.00e+00 3.92e+01
  ... (remaining 14036 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.11: 5912
       24.11 -    48.21: 315
       48.21 -    72.32: 120
       72.32 -    96.43: 17
       96.43 -   120.53: 1
  Dihedral angle restraints: 6365
    sinusoidal: 3212
      harmonic: 3153
  Sorted by residual:
  dihedral pdb=" O4'   G B -14 "
           pdb=" C2'   G B -14 "
           pdb=" C1'   G B -14 "
           pdb=" C3'   G B -14 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00  -20.20   45.20     1      8.00e+00 1.56e-02 4.43e+01
  dihedral pdb=" C5'   G B  21 "
           pdb=" C4'   G B  21 "
           pdb=" C3'   G B  21 "
           pdb=" O3'   G B  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  102.37   44.63     1      8.00e+00 1.56e-02 4.32e+01
  dihedral pdb=" O4'   G B  21 "
           pdb=" C4'   G B  21 "
           pdb=" C3'   G B  21 "
           pdb=" C2'   G B  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -17.13   41.13     1      8.00e+00 1.56e-02 3.70e+01
  ... (remaining 6362 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.132: 1335
       0.132 -    0.264: 214
       0.264 -    0.395: 7
       0.395 -    0.527: 0
       0.527 -    0.659: 3
  Chirality restraints: 1559
  Sorted by residual:
  chirality pdb=" P     A B -24 "
            pdb=" OP1   A B -24 "
            pdb=" OP2   A B -24 "
            pdb=" O5'   A B -24 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.07   -0.66 2.00e-01 2.50e+01 1.09e+01
  chirality pdb=" P     G B -14 "
            pdb=" OP1   G B -14 "
            pdb=" OP2   G B -14 "
            pdb=" O5'   G B -14 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.01   -0.60 2.00e-01 2.50e+01 8.96e+00
  chirality pdb=" P     C B  -9 "
            pdb=" OP1   C B  -9 "
            pdb=" OP2   C B  -9 "
            pdb=" O5'   C B  -9 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    3.01   -0.60 2.00e-01 2.50e+01 8.89e+00
  ... (remaining 1556 not shown)

  Planarity restraints: 1613
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  21 "    0.088 2.00e-02 2.50e+03   3.88e-02 4.51e+01
        pdb=" N9    G B  21 "   -0.059 2.00e-02 2.50e+03
        pdb=" C8    G B  21 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G B  21 "   -0.028 2.00e-02 2.50e+03
        pdb=" C5    G B  21 "   -0.021 2.00e-02 2.50e+03
        pdb=" C6    G B  21 "    0.050 2.00e-02 2.50e+03
        pdb=" O6    G B  21 "    0.026 2.00e-02 2.50e+03
        pdb=" N1    G B  21 "    0.010 2.00e-02 2.50e+03
        pdb=" C2    G B  21 "   -0.029 2.00e-02 2.50e+03
        pdb=" N2    G B  21 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3    G B  21 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G B  21 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  29 "   -0.063 2.00e-02 2.50e+03   3.18e-02 2.78e+01
        pdb=" N9    A B  29 "    0.073 2.00e-02 2.50e+03
        pdb=" C8    A B  29 "   -0.016 2.00e-02 2.50e+03
        pdb=" N7    A B  29 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5    A B  29 "    0.025 2.00e-02 2.50e+03
        pdb=" C6    A B  29 "   -0.008 2.00e-02 2.50e+03
        pdb=" N6    A B  29 "   -0.014 2.00e-02 2.50e+03
        pdb=" N1    A B  29 "   -0.021 2.00e-02 2.50e+03
        pdb=" C2    A B  29 "    0.005 2.00e-02 2.50e+03
        pdb=" N3    A B  29 "    0.009 2.00e-02 2.50e+03
        pdb=" C4    A B  29 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 162 "   -0.068 2.00e-02 2.50e+03   3.49e-02 2.44e+01
        pdb=" CG  TYR A 162 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 162 "    0.035 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 162 "    0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 162 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 162 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 162 "   -0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR A 162 "   -0.039 2.00e-02 2.50e+03
  ... (remaining 1610 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 115
        2.64 -     3.20: 8714
        3.20 -     3.77: 16384
        3.77 -     4.33: 23339
        4.33 -     4.90: 35136
  Nonbonded interactions: 83688
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 345 "
            pdb=" OH  TYR A 439 "
     model   vdw
     2.070 3.040
  nonbonded pdb=" OP1   G B  23 "
            pdb="MG    MG A1101 "
     model   vdw
     2.144 2.170
  nonbonded pdb=" OE1 GLN A 747 "
            pdb="MG    MG A1101 "
     model   vdw
     2.210 2.170
  nonbonded pdb=" ND1 HIS A 282 "
            pdb=" O4    U B  -5 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O   PHE A 406 "
            pdb=" OG  SER A 409 "
     model   vdw
     2.345 3.040
  ... (remaining 83683 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.820
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.770
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
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      :  0.010   0.069  10254  Z= 0.582
  Angle     :  1.722  14.390  14041  Z= 1.100
  Chirality :  0.093   0.659   1559
  Planarity :  0.009   0.092   1613
  Dihedral  : 16.809 120.534   4327
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 0.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  4.05 %
    Favored  : 94.81 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (0.23), residues: 1064
  helix: -1.34 (0.17), residues: 597
  sheet:  0.09 (0.74), residues: 50
  loop :  0.22 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.045   0.005   ARG A 412 
 TYR   0.068   0.009   TYR A 162 
 PHE   0.047   0.009   PHE A 819 
 TRP   0.037   0.010   TRP A 724 
 HIS   0.010   0.004   HIS A 223 

Details of bonding type rmsd
  covalent geometry    : bond        0.00957 (10254)
  covalent geometry    : angle       1.72186 (14041)
  hydrogen bonds       : bond        0.18374 (  537)
  hydrogen bonds       : angle       6.81719 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 176
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8235 (mttt) cc_final: 0.7538 (mttp)
REVERT: A   95 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8053 (mt-10)
REVERT: A  158 MET cc_start: 0.8311 (mtp) cc_final: 0.8004 (mtp)
REVERT: A  172 GLU cc_start: 0.8049 (tt0) cc_final: 0.7545 (mt-10)
REVERT: A  187 LYS cc_start: 0.8540 (mttt) cc_final: 0.8284 (mmtm)
REVERT: A  190 LYS cc_start: 0.7645 (tttt) cc_final: 0.6804 (ptmt)
REVERT: A  202 GLN cc_start: 0.7604 (mt0) cc_final: 0.6758 (mm110)
REVERT: A  220 LYS cc_start: 0.8142 (mttt) cc_final: 0.7440 (mmpt)
REVERT: A  221 LYS cc_start: 0.7947 (mttt) cc_final: 0.7562 (mmtm)
REVERT: A  239 LYS cc_start: 0.8568 (mttt) cc_final: 0.7735 (mmtm)
REVERT: A  248 ARG cc_start: 0.8189 (mmt180) cc_final: 0.7939 (mmt180)
REVERT: A  323 ASP cc_start: 0.6792 (p0) cc_final: 0.6528 (t0)
REVERT: A  380 ARG cc_start: 0.8400 (tpt170) cc_final: 0.8171 (tpt170)
REVERT: A  393 GLU cc_start: 0.8353 (tt0) cc_final: 0.7715 (tp30)
REVERT: A  412 ARG cc_start: 0.8645 (ptt-90) cc_final: 0.7641 (ptt90)
REVERT: A  415 ASP cc_start: 0.8066 (m-30) cc_final: 0.7621 (t70)
REVERT: A  417 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6933 (mm-30)
REVERT: A  419 MET cc_start: 0.7134 (mtm) cc_final: 0.6819 (ttm)
REVERT: A  420 LYS cc_start: 0.7433 (mttt) cc_final: 0.6972 (mptp)
REVERT: A  497 LYS cc_start: 0.8690 (mttt) cc_final: 0.8460 (mmmm)
REVERT: A  514 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8041 (mm-40)
REVERT: A  558 ARG cc_start: 0.7899 (ttt-90) cc_final: 0.7044 (ttp-110)
REVERT: A  570 ARG cc_start: 0.7688 (ttt180) cc_final: 0.7309 (ttm110)
REVERT: A  574 ARG cc_start: 0.8370 (ttt180) cc_final: 0.7468 (ttm110)
REVERT: A  579 ARG cc_start: 0.8290 (mtp180) cc_final: 0.8046 (mtp180)
REVERT: A  580 LYS cc_start: 0.7945 (tttt) cc_final: 0.6954 (ttpp)
REVERT: A  601 LYS cc_start: 0.8524 (tptt) cc_final: 0.8108 (ttmt)
REVERT: A  657 LYS cc_start: 0.8466 (mmtp) cc_final: 0.7547 (mtmt)
REVERT: A  705 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7323 (mm-30)
REVERT: A  725 LYS cc_start: 0.8370 (mttt) cc_final: 0.7692 (mptp)
REVERT: A  786 ASP cc_start: 0.8107 (m-30) cc_final: 0.7843 (t70)
REVERT: A  794 GLN cc_start: 0.8725 (mt0) cc_final: 0.8426 (mp10)
REVERT: A  800 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.7587 (tpm170)
REVERT: A  816 GLN cc_start: 0.8283 (mt0) cc_final: 0.7751 (mm-40)
REVERT: A  817 HIS cc_start: 0.8786 (m170) cc_final: 0.8522 (m90)
REVERT: A  837 GLU cc_start: 0.7643 (tt0) cc_final: 0.6925 (mt-10)
REVERT: A  864 ILE cc_start: 0.7461 (mt) cc_final: 0.7149 (mp)
REVERT: A  867 LYS cc_start: 0.8261 (mttt) cc_final: 0.7307 (tttt)
REVERT: A  941 LYS cc_start: 0.8723 (mttt) cc_final: 0.8101 (mtmt)
REVERT: A  972 GLU cc_start: 0.8258 (tp30) cc_final: 0.7767 (tt0)
REVERT: A  985 MET cc_start: 0.8791 (mtp) cc_final: 0.8558 (mtt)
REVERT: A 1029 LYS cc_start: 0.7608 (tttt) cc_final: 0.6801 (mptt)
REVERT: A 1044 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6448 (tt0)
REVERT: A 1068 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7541 (mp0)
REVERT: A 1070 LYS cc_start: 0.8141 (mttt) cc_final: 0.7479 (mtmt)
  outliers start: 11
  outliers final: 4
  residues processed: 185
  average time/residue: 0.7474
  time to fit residues: 145.1211
Evaluate side-chains
  158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  834 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:   10.0000
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  57 HIS
A  60 ASN
A  63 ASN
A  92 ASN
A 103 GLN
A 153 GLN
A 219 GLN
A 240 GLN
A 256 ASN
A 287 ASN
A 325 ASN
A 710 ASN
A 842 GLN
A 993 GLN
A1004 ASN
A1038 ASN
A1045 GLN
A1054 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.138103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.108470 restraints weight = 22202.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.32
r_work: 0.2927 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2814 r_free = 0.2814    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10254  Z= 0.134
  Angle     :  0.544   6.127  14041  Z= 0.296
  Chirality :  0.040   0.222   1559
  Planarity :  0.004   0.030   1613
  Dihedral  : 16.093 113.789   2045
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  6.12 %
    Favored  : 92.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.25), residues: 1064
  helix:  1.79 (0.20), residues: 606
  sheet: -0.13 (0.70), residues: 49
  loop :  0.64 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 579 
 TYR   0.019   0.002   TYR A 886 
 PHE   0.017   0.002   PHE A 792 
 TRP   0.010   0.001   TRP A 724 
 HIS   0.005   0.001   HIS A 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (10254)
  covalent geometry    : angle       0.54399 (14041)
  hydrogen bonds       : bond        0.05641 (  537)
  hydrogen bonds       : angle       4.13952 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 172
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8348 (mttt) cc_final: 0.7874 (mtmp)
REVERT: A  172 GLU cc_start: 0.8064 (tt0) cc_final: 0.7634 (mt-10)
REVERT: A  190 LYS cc_start: 0.7846 (tttt) cc_final: 0.7317 (ptpt)
REVERT: A  202 GLN cc_start: 0.7701 (mt0) cc_final: 0.7107 (mm110)
REVERT: A  220 LYS cc_start: 0.8651 (mttt) cc_final: 0.8250 (mmpt)
REVERT: A  221 LYS cc_start: 0.8302 (mttt) cc_final: 0.8043 (mmtm)
REVERT: A  239 LYS cc_start: 0.8324 (mttt) cc_final: 0.7699 (mmtm)
REVERT: A  393 GLU cc_start: 0.8168 (tt0) cc_final: 0.7861 (tp30)
REVERT: A  412 ARG cc_start: 0.8505 (ptt-90) cc_final: 0.7852 (ptt90)
REVERT: A  419 MET cc_start: 0.7761 (mtm) cc_final: 0.7412 (mtm)
REVERT: A  420 LYS cc_start: 0.7897 (mttt) cc_final: 0.7690 (mptp)
REVERT: A  533 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7931 (tp30)
REVERT: A  558 ARG cc_start: 0.7776 (ttt-90) cc_final: 0.7246 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8373 (tttt) cc_final: 0.7607 (ttpp)
REVERT: A  574 ARG cc_start: 0.8376 (ttt180) cc_final: 0.7782 (ttm110)
REVERT: A  579 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7773 (mtp180)
REVERT: A  657 LYS cc_start: 0.8564 (mmtp) cc_final: 0.7816 (mppt)
REVERT: A  705 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7905 (mm-30)
REVERT: A  725 LYS cc_start: 0.8313 (mttt) cc_final: 0.7853 (mptp)
REVERT: A  794 GLN cc_start: 0.8411 (mt0) cc_final: 0.8083 (mp10)
REVERT: A  800 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7881 (tpm170)
REVERT: A  816 GLN cc_start: 0.8457 (mt0) cc_final: 0.8014 (mm-40)
REVERT: A  837 GLU cc_start: 0.8010 (tt0) cc_final: 0.7594 (tp30)
REVERT: A  867 LYS cc_start: 0.8421 (mttt) cc_final: 0.7799 (tttt)
REVERT: A  985 MET cc_start: 0.8650 (mtp) cc_final: 0.8382 (mtt)
REVERT: A 1029 LYS cc_start: 0.7700 (tttt) cc_final: 0.7217 (mppt)
REVERT: A 1068 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7586 (mp0)
REVERT: A 1070 LYS cc_start: 0.8339 (mttt) cc_final: 0.7993 (mtmt)
REVERT: A 1089 MET cc_start: 0.7705 (mmt) cc_final: 0.7494 (mmt)
  outliers start: 9
  outliers final: 4
  residues processed: 179
  average time/residue: 0.8411
  time to fit residues: 157.9068
Evaluate side-chains
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 152
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  834 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 104 optimal weight:    0.2980
   chunk 69 optimal weight:    0.0060
   chunk 106 optimal weight:    9.9990
   chunk 60 optimal weight:    0.1980
   chunk 96 optimal weight:    0.0040
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.2608

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  92 ASN
A 103 GLN
A 171 ASN
A 219 GLN
A 240 GLN
A 596 GLN
A 710 ASN
A 842 GLN
A1038 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.145142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.116074 restraints weight = 23977.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.51
r_work: 0.2995 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2914 r_free = 0.2914    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.2512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10254  Z= 0.095
  Angle     :  0.446   5.254  14041  Z= 0.240
  Chirality :  0.036   0.163   1559
  Planarity :  0.003   0.033   1613
  Dihedral  : 15.784 107.985   2045
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  7.47 %
    Favored  : 91.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.66 (0.25), residues: 1064
  helix:  2.60 (0.20), residues: 610
  sheet:  0.20 (0.72), residues: 51
  loop :  0.76 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 579 
 TYR   0.015   0.001   TYR A  17 
 PHE   0.014   0.001   PHE A 792 
 TRP   0.007   0.001   TRP A 724 
 HIS   0.003   0.000   HIS A 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00182 (10254)
  covalent geometry    : angle       0.44597 (14041)
  hydrogen bonds       : bond        0.04318 (  537)
  hydrogen bonds       : angle       3.75383 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 169
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 ILE cc_start: 0.8740 (mt) cc_final: 0.8471 (mt)
REVERT: A   34 LYS cc_start: 0.8198 (mttt) cc_final: 0.7896 (mtmm)
REVERT: A  140 LYS cc_start: 0.7895 (mttt) cc_final: 0.7607 (mttm)
REVERT: A  172 GLU cc_start: 0.7959 (tt0) cc_final: 0.7482 (mt-10)
REVERT: A  190 LYS cc_start: 0.7754 (tttt) cc_final: 0.7303 (ptpt)
REVERT: A  202 GLN cc_start: 0.7534 (mt0) cc_final: 0.6935 (mm110)
REVERT: A  220 LYS cc_start: 0.8573 (mttt) cc_final: 0.8216 (mmpt)
REVERT: A  221 LYS cc_start: 0.8301 (mttt) cc_final: 0.8018 (mmtm)
REVERT: A  239 LYS cc_start: 0.8193 (mttt) cc_final: 0.7605 (mmtm)
REVERT: A  393 GLU cc_start: 0.8130 (tt0) cc_final: 0.7857 (tp30)
REVERT: A  412 ARG cc_start: 0.8579 (ptt-90) cc_final: 0.7904 (ptt90)
REVERT: A  420 LYS cc_start: 0.7822 (mttt) cc_final: 0.7521 (mptp)
REVERT: A  558 ARG cc_start: 0.7638 (ttt-90) cc_final: 0.7179 (ttp-110)
REVERT: A  574 ARG cc_start: 0.8415 (ttt180) cc_final: 0.7733 (ttm110)
REVERT: A  608 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8365 (ttmt)
REVERT: A  705 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7820 (mm-30)
REVERT: A  710 ASN cc_start: 0.8420 (m-40) cc_final: 0.8204 (m110)
REVERT: A  725 LYS cc_start: 0.8138 (mttt) cc_final: 0.7769 (mptp)
REVERT: A  794 GLN cc_start: 0.8450 (mt0) cc_final: 0.8173 (mp10)
REVERT: A  800 ARG cc_start: 0.8066 (ttp-110) cc_final: 0.7772 (tpm170)
REVERT: A  816 GLN cc_start: 0.8337 (mt0) cc_final: 0.7893 (mm-40)
REVERT: A  841 LYS cc_start: 0.7461 (tttp) cc_final: 0.6972 (mtmt)
REVERT: A  867 LYS cc_start: 0.8230 (mttt) cc_final: 0.7602 (tttm)
REVERT: A 1029 LYS cc_start: 0.7519 (tttt) cc_final: 0.7132 (mppt)
REVERT: A 1068 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7464 (mp0)
REVERT: A 1070 LYS cc_start: 0.8212 (mttt) cc_final: 0.7876 (mtmt)
  outliers start: 9
  outliers final: 5
  residues processed: 173
  average time/residue: 0.8302
  time to fit residues: 150.6292
Evaluate side-chains
  159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 154
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  380 ARG
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  927 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 109 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 89 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 103 GLN
A 219 GLN
A 428 ASN
A 549 HIS
A 596 GLN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.139298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.110897 restraints weight = 13478.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.45
r_work: 0.3021 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10254  Z= 0.129
  Angle     :  0.486   5.351  14041  Z= 0.262
  Chirality :  0.039   0.167   1559
  Planarity :  0.004   0.032   1613
  Dihedral  : 15.856 108.653   2044
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.20 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.64 (0.25), residues: 1064
  helix:  2.55 (0.20), residues: 608
  sheet:  0.74 (0.79), residues: 44
  loop :  0.75 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 695 
 TYR   0.021   0.002   TYR A  17 
 PHE   0.017   0.001   PHE A 792 
 TRP   0.004   0.001   TRP A 724 
 HIS   0.004   0.001   HIS A 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10254)
  covalent geometry    : angle       0.48552 (14041)
  hydrogen bonds       : bond        0.05151 (  537)
  hydrogen bonds       : angle       3.82677 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8325 (mttt) cc_final: 0.7926 (mtmm)
REVERT: A  172 GLU cc_start: 0.8090 (tt0) cc_final: 0.7640 (mt-10)
REVERT: A  190 LYS cc_start: 0.7807 (tttt) cc_final: 0.7368 (ptpt)
REVERT: A  202 GLN cc_start: 0.7577 (mt0) cc_final: 0.6990 (mm110)
REVERT: A  220 LYS cc_start: 0.8598 (mttt) cc_final: 0.8297 (mmpt)
REVERT: A  221 LYS cc_start: 0.8383 (mttt) cc_final: 0.8101 (mmtm)
REVERT: A  239 LYS cc_start: 0.8301 (mttt) cc_final: 0.7704 (mmtm)
REVERT: A  393 GLU cc_start: 0.8218 (tt0) cc_final: 0.7933 (tp30)
REVERT: A  412 ARG cc_start: 0.8607 (ptt-90) cc_final: 0.7952 (ptt90)
REVERT: A  420 LYS cc_start: 0.7787 (mttt) cc_final: 0.7554 (mptp)
REVERT: A  533 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7901 (tp30)
REVERT: A  558 ARG cc_start: 0.7768 (ttt-90) cc_final: 0.7267 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8368 (tttt) cc_final: 0.7615 (ttpp)
REVERT: A  574 ARG cc_start: 0.8467 (ttt180) cc_final: 0.7807 (ttm110)
REVERT: A  589 MET cc_start: 0.8833 (ttt) cc_final: 0.8392 (ttt)
REVERT: A  705 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7833 (mm-30)
REVERT: A  710 ASN cc_start: 0.8388 (m-40) cc_final: 0.8181 (m110)
REVERT: A  725 LYS cc_start: 0.8336 (mttt) cc_final: 0.7888 (mptp)
REVERT: A  794 GLN cc_start: 0.8431 (mt0) cc_final: 0.8161 (mp10)
REVERT: A  800 ARG cc_start: 0.8188 (ttp-110) cc_final: 0.7853 (tpm170)
REVERT: A  816 GLN cc_start: 0.8430 (mt0) cc_final: 0.7965 (mm110)
REVERT: A  841 LYS cc_start: 0.7634 (tttp) cc_final: 0.7091 (mtmt)
REVERT: A  867 LYS cc_start: 0.8336 (mttt) cc_final: 0.7660 (tttm)
REVERT: A  908 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.6080 (t0)
REVERT: A 1029 LYS cc_start: 0.7625 (tttt) cc_final: 0.7237 (mppt)
REVERT: A 1068 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7525 (mp0)
REVERT: A 1070 LYS cc_start: 0.8302 (mttt) cc_final: 0.7911 (mtmt)
  outliers start: 12
  outliers final: 6
  residues processed: 160
  average time/residue: 0.8883
  time to fit residues: 148.9644
Evaluate side-chains
  155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 147
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  518 LYS
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  737 SER
Chi-restraints excluded: chain A residue  908 ASP
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 18 optimal weight:    0.2980
   chunk 61 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 68 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 103 GLN
A 171 ASN
A 219 GLN
A 325 ASN
A 596 GLN
A 842 GLN
A 954 ASN
A1004 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.138190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.108542 restraints weight = 21834.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.31
r_work: 0.2919 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2944
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2944 r_free = 0.2944    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2944
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10254  Z= 0.142
  Angle     :  0.499   5.394  14041  Z= 0.269
  Chirality :  0.039   0.168   1559
  Planarity :  0.004   0.033   1613
  Dihedral  : 15.956 108.115   2043
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  8.09 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.54 (0.25), residues: 1064
  helix:  2.44 (0.20), residues: 607
  sheet:  0.78 (0.80), residues: 44
  loop :  0.74 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 695 
 TYR   0.022   0.002   TYR A  17 
 PHE   0.018   0.002   PHE A 792 
 TRP   0.004   0.001   TRP A 724 
 HIS   0.005   0.001   HIS A 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (10254)
  covalent geometry    : angle       0.49856 (14041)
  hydrogen bonds       : bond        0.05394 (  537)
  hydrogen bonds       : angle       3.86009 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8337 (mttt) cc_final: 0.7945 (mtmm)
REVERT: A  172 GLU cc_start: 0.8035 (tt0) cc_final: 0.7599 (mt-10)
REVERT: A  190 LYS cc_start: 0.7778 (tttt) cc_final: 0.7390 (ptpt)
REVERT: A  202 GLN cc_start: 0.7666 (mt0) cc_final: 0.7046 (mm110)
REVERT: A  220 LYS cc_start: 0.8599 (mttt) cc_final: 0.8309 (mmpt)
REVERT: A  221 LYS cc_start: 0.8404 (mttt) cc_final: 0.8101 (mmtm)
REVERT: A  239 LYS cc_start: 0.8299 (mttt) cc_final: 0.7694 (mmtm)
REVERT: A  393 GLU cc_start: 0.8206 (tt0) cc_final: 0.7942 (tp30)
REVERT: A  412 ARG cc_start: 0.8575 (ptt-90) cc_final: 0.7924 (ptt90)
REVERT: A  420 LYS cc_start: 0.7754 (mttt) cc_final: 0.7385 (tttm)
REVERT: A  533 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7878 (tp30)
REVERT: A  558 ARG cc_start: 0.7761 (ttt-90) cc_final: 0.7283 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8363 (tttt) cc_final: 0.7586 (ttpp)
REVERT: A  574 ARG cc_start: 0.8471 (ttt180) cc_final: 0.7785 (ttm110)
REVERT: A  705 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7843 (mm-30)
REVERT: A  725 LYS cc_start: 0.8290 (mttt) cc_final: 0.7946 (mptp)
REVERT: A  794 GLN cc_start: 0.8410 (mt0) cc_final: 0.8139 (mp10)
REVERT: A  800 ARG cc_start: 0.8155 (ttp-110) cc_final: 0.7828 (tpm170)
REVERT: A  841 LYS cc_start: 0.7724 (tttp) cc_final: 0.7162 (mtmt)
REVERT: A  867 LYS cc_start: 0.8326 (mttt) cc_final: 0.7673 (tttt)
REVERT: A 1029 LYS cc_start: 0.7625 (tttt) cc_final: 0.7208 (mppt)
REVERT: A 1068 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7587 (mp0)
REVERT: A 1070 LYS cc_start: 0.8282 (mttt) cc_final: 0.7896 (mtmt)
  outliers start: 14
  outliers final: 8
  residues processed: 160
  average time/residue: 0.8951
  time to fit residues: 150.2561
Evaluate side-chains
  155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  737 SER
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 85 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 107 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 103 GLN
A 219 GLN
A 325 ASN
A 596 GLN
A 710 ASN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.139902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.110253 restraints weight = 19433.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.05
r_work: 0.2962 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2737
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2737 r_free = 0.2737    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2737
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8758
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10254  Z= 0.120
  Angle     :  0.467   5.443  14041  Z= 0.251
  Chirality :  0.038   0.151   1559
  Planarity :  0.004   0.032   1613
  Dihedral  : 15.864 106.022   2043
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.61 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.59 (0.25), residues: 1064
  helix:  2.51 (0.20), residues: 609
  sheet:  0.45 (0.82), residues: 42
  loop :  0.75 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 695 
 TYR   0.020   0.001   TYR A  17 
 PHE   0.017   0.001   PHE A 792 
 TRP   0.005   0.001   TRP A 724 
 HIS   0.004   0.001   HIS A 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10254)
  covalent geometry    : angle       0.46674 (14041)
  hydrogen bonds       : bond        0.04953 (  537)
  hydrogen bonds       : angle       3.77655 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8385 (mttt) cc_final: 0.8068 (mtmm)
REVERT: A  172 GLU cc_start: 0.8082 (tt0) cc_final: 0.7607 (mt-10)
REVERT: A  190 LYS cc_start: 0.7831 (tttt) cc_final: 0.7384 (ptpt)
REVERT: A  202 GLN cc_start: 0.7693 (mt0) cc_final: 0.7039 (mm110)
REVERT: A  220 LYS cc_start: 0.8604 (mttt) cc_final: 0.8278 (mmpt)
REVERT: A  221 LYS cc_start: 0.8481 (mttt) cc_final: 0.8091 (mmtm)
REVERT: A  239 LYS cc_start: 0.8337 (mttt) cc_final: 0.7759 (mmtm)
REVERT: A  393 GLU cc_start: 0.8330 (tt0) cc_final: 0.7967 (tp30)
REVERT: A  412 ARG cc_start: 0.8724 (ptt-90) cc_final: 0.8016 (ptt90)
REVERT: A  420 LYS cc_start: 0.7759 (mttt) cc_final: 0.7307 (tttm)
REVERT: A  453 LYS cc_start: 0.8517 (mttp) cc_final: 0.8013 (mmpt)
REVERT: A  533 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7917 (tp30)
REVERT: A  558 ARG cc_start: 0.7800 (ttt-90) cc_final: 0.7249 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8387 (tttt) cc_final: 0.7604 (ttpp)
REVERT: A  574 ARG cc_start: 0.8556 (ttt180) cc_final: 0.7841 (ttm110)
REVERT: A  705 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7932 (mm-30)
REVERT: A  725 LYS cc_start: 0.8380 (mttt) cc_final: 0.8004 (mptp)
REVERT: A  794 GLN cc_start: 0.8560 (mt0) cc_final: 0.8284 (mp10)
REVERT: A  800 ARG cc_start: 0.8337 (ttp-110) cc_final: 0.7915 (tpm170)
REVERT: A  841 LYS cc_start: 0.7720 (tttp) cc_final: 0.7110 (mtmt)
REVERT: A  867 LYS cc_start: 0.8359 (mttt) cc_final: 0.7650 (tttm)
REVERT: A 1029 LYS cc_start: 0.7630 (tttt) cc_final: 0.7203 (mppt)
REVERT: A 1068 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7617 (mp0)
REVERT: A 1070 LYS cc_start: 0.8282 (mttt) cc_final: 0.7894 (mtmt)
  outliers start: 12
  outliers final: 9
  residues processed: 156
  average time/residue: 0.9252
  time to fit residues: 151.1621
Evaluate side-chains
  159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  518 LYS
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  737 SER
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 68 optimal weight:    0.4980
   chunk 56 optimal weight:    5.9990
   chunk 102 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 103 GLN
A 171 ASN
A 219 GLN
A 325 ASN
A 596 GLN
A 710 ASN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.137766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.107974 restraints weight = 20057.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.14
r_work: 0.2928 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10254  Z= 0.145
  Angle     :  0.496   5.383  14041  Z= 0.267
  Chirality :  0.039   0.152   1559
  Planarity :  0.004   0.036   1613
  Dihedral  : 15.919 106.644   2043
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  8.20 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.25), residues: 1064
  helix:  2.44 (0.20), residues: 608
  sheet:  0.45 (0.82), residues: 42
  loop :  0.75 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 695 
 TYR   0.022   0.002   TYR A  17 
 PHE   0.018   0.002   PHE A 792 
 TRP   0.003   0.001   TRP A 724 
 HIS   0.005   0.001   HIS A 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (10254)
  covalent geometry    : angle       0.49632 (14041)
  hydrogen bonds       : bond        0.05384 (  537)
  hydrogen bonds       : angle       3.85076 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.8282 (mttt) cc_final: 0.7963 (mtmm)
REVERT: A  172 GLU cc_start: 0.8005 (tt0) cc_final: 0.7599 (mt-10)
REVERT: A  190 LYS cc_start: 0.7699 (tttt) cc_final: 0.7373 (ptpt)
REVERT: A  202 GLN cc_start: 0.7661 (mt0) cc_final: 0.7056 (mm110)
REVERT: A  220 LYS cc_start: 0.8610 (mttt) cc_final: 0.8363 (mmpt)
REVERT: A  221 LYS cc_start: 0.8474 (mttt) cc_final: 0.8126 (mmtm)
REVERT: A  239 LYS cc_start: 0.8279 (mttt) cc_final: 0.7717 (mmtm)
REVERT: A  248 ARG cc_start: 0.8524 (mmt180) cc_final: 0.8253 (mmt180)
REVERT: A  393 GLU cc_start: 0.8149 (tt0) cc_final: 0.7920 (tp30)
REVERT: A  412 ARG cc_start: 0.8521 (ptt-90) cc_final: 0.7896 (ptt90)
REVERT: A  420 LYS cc_start: 0.7731 (mttt) cc_final: 0.7379 (tttm)
REVERT: A  453 LYS cc_start: 0.8554 (mttp) cc_final: 0.8128 (mmtm)
REVERT: A  533 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7864 (tp30)
REVERT: A  558 ARG cc_start: 0.7706 (ttt-90) cc_final: 0.7256 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8350 (tttt) cc_final: 0.7570 (ttpp)
REVERT: A  574 ARG cc_start: 0.8442 (ttt180) cc_final: 0.7750 (ttm110)
REVERT: A  705 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7781 (mm-30)
REVERT: A  725 LYS cc_start: 0.8290 (mttt) cc_final: 0.7988 (mptp)
REVERT: A  794 GLN cc_start: 0.8333 (mt0) cc_final: 0.8075 (mp10)
REVERT: A  800 ARG cc_start: 0.8075 (ttp-110) cc_final: 0.7787 (tpm170)
REVERT: A  841 LYS cc_start: 0.7708 (tttp) cc_final: 0.7145 (mtmt)
REVERT: A  867 LYS cc_start: 0.8327 (mttt) cc_final: 0.7680 (tttt)
REVERT: A  941 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8383 (mttp)
REVERT: A 1029 LYS cc_start: 0.7636 (tttt) cc_final: 0.7210 (mppt)
REVERT: A 1068 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7557 (mp0)
REVERT: A 1070 LYS cc_start: 0.8270 (mttt) cc_final: 0.7890 (mtmt)
  outliers start: 14
  outliers final: 9
  residues processed: 157
  average time/residue: 0.9113
  time to fit residues: 149.9491
Evaluate side-chains
  158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 MET
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  737 SER
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue  941 LYS
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 83 optimal weight:    6.9990
   chunk 13 optimal weight:    0.4980
   chunk 4 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 88 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0980
   chunk 91 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A  92 ASN
A 103 GLN
A 219 GLN
A 596 GLN
A 710 ASN
A 842 GLN
A1004 ASN
A1038 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.143871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.114436 restraints weight = 21710.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.28
r_work: 0.2992 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10254  Z= 0.094
  Angle     :  0.425   5.251  14041  Z= 0.229
  Chirality :  0.036   0.152   1559
  Planarity :  0.003   0.036   1613
  Dihedral  : 15.746 102.945   2043
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  8.82 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.77 (0.25), residues: 1064
  helix:  2.66 (0.20), residues: 611
  sheet:  0.79 (0.84), residues: 44
  loop :  0.77 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 695 
 TYR   0.017   0.001   TYR A  17 
 PHE   0.014   0.001   PHE A 792 
 TRP   0.005   0.001   TRP A 724 
 HIS   0.003   0.001   HIS A 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 (10254)
  covalent geometry    : angle       0.42467 (14041)
  hydrogen bonds       : bond        0.04305 (  537)
  hydrogen bonds       : angle       3.63673 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7924 (tt0) cc_final: 0.7485 (mt-10)
REVERT: A  190 LYS cc_start: 0.7603 (tttt) cc_final: 0.7302 (ptpt)
REVERT: A  202 GLN cc_start: 0.7621 (mt0) cc_final: 0.7022 (mm110)
REVERT: A  220 LYS cc_start: 0.8602 (mttt) cc_final: 0.8332 (mmpt)
REVERT: A  221 LYS cc_start: 0.8452 (mttt) cc_final: 0.8078 (mmtm)
REVERT: A  239 LYS cc_start: 0.8224 (mttt) cc_final: 0.7670 (mmtm)
REVERT: A  248 ARG cc_start: 0.8538 (mmt180) cc_final: 0.8328 (mmt180)
REVERT: A  393 GLU cc_start: 0.8162 (tt0) cc_final: 0.7923 (tp30)
REVERT: A  412 ARG cc_start: 0.8524 (ptt-90) cc_final: 0.7908 (ptt90)
REVERT: A  420 LYS cc_start: 0.7698 (mttt) cc_final: 0.7337 (tttm)
REVERT: A  453 LYS cc_start: 0.8522 (mttp) cc_final: 0.8077 (mmpt)
REVERT: A  533 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7885 (tp30)
REVERT: A  558 ARG cc_start: 0.7699 (ttt-90) cc_final: 0.7242 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8353 (tttt) cc_final: 0.7593 (ttpp)
REVERT: A  574 ARG cc_start: 0.8482 (ttt180) cc_final: 0.7789 (ttm110)
REVERT: A  705 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7820 (mm-30)
REVERT: A  710 ASN cc_start: 0.8316 (m-40) cc_final: 0.8097 (m110)
REVERT: A  725 LYS cc_start: 0.8197 (mttt) cc_final: 0.7894 (mptp)
REVERT: A  794 GLN cc_start: 0.8332 (mt0) cc_final: 0.8081 (mp10)
REVERT: A  800 ARG cc_start: 0.8066 (ttp-110) cc_final: 0.7766 (tpm170)
REVERT: A  841 LYS cc_start: 0.7726 (tttp) cc_final: 0.7104 (mtmt)
REVERT: A  867 LYS cc_start: 0.8262 (mttt) cc_final: 0.7615 (tttm)
REVERT: A 1007 LYS cc_start: 0.7813 (tttp) cc_final: 0.7515 (tttp)
REVERT: A 1029 LYS cc_start: 0.7646 (tttt) cc_final: 0.7210 (mppt)
REVERT: A 1068 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7512 (mp0)
REVERT: A 1070 LYS cc_start: 0.8186 (mttt) cc_final: 0.7842 (mtmt)
REVERT: A 1085 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8034 (mt-10)
  outliers start: 10
  outliers final: 8
  residues processed: 163
  average time/residue: 0.7209
  time to fit residues: 123.3156
Evaluate side-chains
  160 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  737 SER
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1004 ASN
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0970
   chunk 20 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 103 GLN
A 219 GLN
A 596 GLN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.141913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.112828 restraints weight = 20973.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.18
r_work: 0.3159 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2961
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10254  Z= 0.107
  Angle     :  0.446   5.398  14041  Z= 0.240
  Chirality :  0.037   0.147   1559
  Planarity :  0.004   0.042   1613
  Dihedral  : 15.685 103.653   2043
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  9.44 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.73 (0.25), residues: 1064
  helix:  2.63 (0.20), residues: 610
  sheet:  0.79 (0.84), residues: 44
  loop :  0.77 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 695 
 TYR   0.020   0.001   TYR A  17 
 PHE   0.016   0.001   PHE A 792 
 TRP   0.005   0.001   TRP A 724 
 HIS   0.004   0.001   HIS A 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (10254)
  covalent geometry    : angle       0.44564 (14041)
  hydrogen bonds       : bond        0.04651 (  537)
  hydrogen bonds       : angle       3.67590 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 150
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7124 (mptt)
REVERT: A  172 GLU cc_start: 0.8052 (tt0) cc_final: 0.7586 (mt-10)
REVERT: A  190 LYS cc_start: 0.7603 (tttt) cc_final: 0.7247 (ptpt)
REVERT: A  202 GLN cc_start: 0.7674 (mt0) cc_final: 0.6999 (mm110)
REVERT: A  220 LYS cc_start: 0.8559 (mttt) cc_final: 0.8249 (mmpt)
REVERT: A  221 LYS cc_start: 0.8449 (mttt) cc_final: 0.8006 (mmtm)
REVERT: A  239 LYS cc_start: 0.8253 (mttt) cc_final: 0.7665 (mmtm)
REVERT: A  248 ARG cc_start: 0.8531 (mmt180) cc_final: 0.8328 (mmt180)
REVERT: A  393 GLU cc_start: 0.8255 (tt0) cc_final: 0.7919 (tp30)
REVERT: A  412 ARG cc_start: 0.8616 (ptt-90) cc_final: 0.7962 (ptt90)
REVERT: A  420 LYS cc_start: 0.7609 (mttt) cc_final: 0.7280 (tttm)
REVERT: A  453 LYS cc_start: 0.8528 (mttp) cc_final: 0.8018 (mmpt)
REVERT: A  558 ARG cc_start: 0.7792 (ttt-90) cc_final: 0.7242 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8346 (tttt) cc_final: 0.7563 (ttpp)
REVERT: A  574 ARG cc_start: 0.8507 (ttt180) cc_final: 0.7778 (ttm110)
REVERT: A  705 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7802 (mm-30)
REVERT: A  710 ASN cc_start: 0.8266 (m-40) cc_final: 0.7998 (m110)
REVERT: A  725 LYS cc_start: 0.8239 (mttt) cc_final: 0.7911 (mptp)
REVERT: A  794 GLN cc_start: 0.8378 (mt0) cc_final: 0.8095 (mp10)
REVERT: A  800 ARG cc_start: 0.8214 (ttp-110) cc_final: 0.7822 (tpm170)
REVERT: A  841 LYS cc_start: 0.7775 (tttp) cc_final: 0.7106 (mtmt)
REVERT: A  867 LYS cc_start: 0.8301 (mttt) cc_final: 0.7590 (tttm)
REVERT: A 1007 LYS cc_start: 0.7786 (tttp) cc_final: 0.7481 (tttp)
REVERT: A 1029 LYS cc_start: 0.7630 (tttt) cc_final: 0.7187 (mppt)
REVERT: A 1068 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7580 (mp0)
REVERT: A 1070 LYS cc_start: 0.8201 (mttt) cc_final: 0.7822 (mtmt)
REVERT: A 1085 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8106 (mt-10)
  outliers start: 7
  outliers final: 8
  residues processed: 156
  average time/residue: 0.8445
  time to fit residues: 138.1049
Evaluate side-chains
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 149
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  737 SER
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1004 ASN
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 95 optimal weight:    7.9990
   chunk 57 optimal weight:    0.0270
   chunk 28 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.5642

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 103 GLN
A 219 GLN
A 596 GLN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.138087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.107798 restraints weight = 24356.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.43
r_work: 0.2903 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10254  Z= 0.161
  Angle     :  0.516   5.527  14041  Z= 0.277
  Chirality :  0.040   0.153   1559
  Planarity :  0.004   0.051   1613
  Dihedral  : 15.782 106.060   2043
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.44 %
    Favored  : 89.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.25), residues: 1064
  helix:  2.40 (0.20), residues: 609
  sheet:  0.41 (0.83), residues: 42
  loop :  0.75 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 695 
 TYR   0.023   0.002   TYR A  17 
 PHE   0.019   0.002   PHE A 792 
 TRP   0.002   0.001   TRP A  50 
 HIS   0.005   0.001   HIS A 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (10254)
  covalent geometry    : angle       0.51571 (14041)
  hydrogen bonds       : bond        0.05551 (  537)
  hydrogen bonds       : angle       3.86756 ( 1473)

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

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

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2128 Ramachandran restraints generated.
    1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7025 (mptt)
REVERT: A  172 GLU cc_start: 0.8004 (tt0) cc_final: 0.7593 (mt-10)
REVERT: A  190 LYS cc_start: 0.7612 (tttt) cc_final: 0.7285 (ptpt)
REVERT: A  202 GLN cc_start: 0.7647 (mt0) cc_final: 0.7022 (mm110)
REVERT: A  220 LYS cc_start: 0.8599 (mttt) cc_final: 0.8367 (mmpt)
REVERT: A  221 LYS cc_start: 0.8465 (mttt) cc_final: 0.8118 (mmtm)
REVERT: A  239 LYS cc_start: 0.8342 (mttt) cc_final: 0.7751 (mmtm)
REVERT: A  393 GLU cc_start: 0.8186 (tt0) cc_final: 0.7939 (tp30)
REVERT: A  412 ARG cc_start: 0.8564 (ptt-90) cc_final: 0.7935 (ptt90)
REVERT: A  453 LYS cc_start: 0.8554 (mttp) cc_final: 0.8107 (mmtm)
REVERT: A  533 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7858 (tp30)
REVERT: A  558 ARG cc_start: 0.7725 (ttt-90) cc_final: 0.7256 (ttp-110)
REVERT: A  573 LYS cc_start: 0.8364 (tttt) cc_final: 0.7582 (ttpp)
REVERT: A  574 ARG cc_start: 0.8472 (ttt180) cc_final: 0.7774 (ttm110)
REVERT: A  705 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7785 (mm-30)
REVERT: A  725 LYS cc_start: 0.8284 (mttt) cc_final: 0.7973 (mptp)
REVERT: A  794 GLN cc_start: 0.8399 (mt0) cc_final: 0.8140 (mp10)
REVERT: A  800 ARG cc_start: 0.8140 (ttp-110) cc_final: 0.7821 (tpm170)
REVERT: A  841 LYS cc_start: 0.7738 (tttp) cc_final: 0.7149 (mtmt)
REVERT: A  867 LYS cc_start: 0.8364 (mttt) cc_final: 0.7694 (tttt)
REVERT: A 1029 LYS cc_start: 0.7682 (tttt) cc_final: 0.7399 (mptt)
REVERT: A 1068 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7589 (mp0)
REVERT: A 1070 LYS cc_start: 0.8242 (mttt) cc_final: 0.7879 (mtmt)
  outliers start: 8
  outliers final: 7
  residues processed: 153
  average time/residue: 0.9394
  time to fit residues: 150.5823
Evaluate side-chains
  154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  737 SER
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue  927 SER
Chi-restraints excluded: chain A residue 1067 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 85 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 86 optimal weight:    0.8980
   chunk 104 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 103 GLN
A 171 ASN
A 219 GLN
A 596 GLN
A 710 ASN
A 842 GLN
A1004 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.140222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.110500 restraints weight = 28472.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.72
r_work: 0.3117 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10254  Z= 0.117
  Angle     :  0.461   5.518  14041  Z= 0.248
  Chirality :  0.037   0.146   1559
  Planarity :  0.004   0.041   1613
  Dihedral  : 15.673 104.410   2043
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.75 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.59 (0.25), residues: 1064
  helix:  2.52 (0.20), residues: 609
  sheet:  0.42 (0.84), residues: 42
  loop :  0.75 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 695 
 TYR   0.020   0.001   TYR A  17 
 PHE   0.016   0.001   PHE A 792 
 TRP   0.004   0.001   TRP A 724 
 HIS   0.004   0.001   HIS A 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (10254)
  covalent geometry    : angle       0.46122 (14041)
  hydrogen bonds       : bond        0.04900 (  537)
  hydrogen bonds       : angle       3.75517 ( 1473)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3970.90 seconds
wall clock time: 68 minutes 17.11 seconds (4097.11 seconds total)