Starting phenix.real_space_refine
on Thu Aug  6 03:17:55 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8ja0_36123/08_2026/8ja0_36123.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ja0_36123/08_2026/8ja0_36123.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8ja0_36123/08_2026/8ja0_36123.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8ja0_36123/08_2026/8ja0_36123.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ja0_36123/08_2026/8ja0_36123.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ja0_36123/08_2026/8ja0_36123.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ja0_36123/08_2026/8ja0_36123.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ja0_36123/08_2026/8ja0_36123.cif"
  }
  resolution = 3.52
  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=  -0.001 sd=   0.171
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2216 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     115      5.49       5
     S      25      5.16       5
     C    6695      2.51       5
     N    2028      2.21       5
     O    2428      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11291
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 8168
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1027, 8144
          Classifications: {'peptide': 1027}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 43, 'TRANS': 983}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 198
          Unresolved non-hydrogen angles: 234
          Unresolved non-hydrogen dihedrals: 170
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 9, 'HIS:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 113
      Conformer: "B"
        Number of residues, atoms: 1027, 8144
          Classifications: {'peptide': 1027}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 43, 'TRANS': 983}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 198
          Unresolved non-hydrogen angles: 234
          Unresolved non-hydrogen dihedrals: 170
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 9, 'HIS:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 113
          bond proxies already assigned to first conformer: 8271
    Chain: "D"
      Number of atoms: 692
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 692
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 2, 'TRANS': 84}
    Chain: "B"
      Number of atoms: 2431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 2431
          Classifications: {'RNAv2': 115}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 47, 'rna3p_pyr': 57}
          Link IDs: {'rna2p': 11, 'rna3p': 103}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG A 398 " occ=0.39
      ... (20 atoms not shown)
      pdb=" NH2BARG A 398 " occ=0.61
    residue:
      pdb=" N  AARG A 538 " occ=0.87
      ... (20 atoms not shown)
      pdb=" NH2BARG A 538 " occ=0.13
  Time building chain proxies: 3.63, per 1000 atoms: 0.32
  Number of scatterers: 11291
  At special positions: 0
  Unit cell: (108.8, 111.35, 141.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     P     115     15.00
     O    2428      8.00
     N    2028      7.00
     C    6695      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: 0.92
  Conformation dependent library (CDL) restraints added in 657.4 milliseconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2108

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 9 sheets defined
      45.8% alpha, 8.9% beta
      35 base pairs and 62 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 89
    Processing helix  chain 'A' and resid 93 through 97
    Processing helix  chain 'A' and resid 109 through 115
    Processing helix  chain 'A' and resid 123 through 137
      removed outlier: 3.756A  pdb=" N   SER A 128 " --> pdb=" O   PRO A 124 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ALA A 129 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   VAL A 130 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 170
    Processing helix  chain 'A' and resid 176 through 184
    Processing helix  chain 'A' and resid 204 through 223
      removed outlier: 3.819A  pdb=" N   PHE A 222 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 240
    Processing helix  chain 'A' and resid 271 through 285
      removed outlier: 3.935A  pdb=" N   ASN A 285 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 306
      removed outlier: 4.002A  pdb=" N   THR A 304 " --> pdb=" O   THR A 300 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   MET A 306 " --> pdb=" O   ARG A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 325
      removed outlier: 3.755A  pdb=" N   ALA A 320 " --> pdb=" O   THR A 316 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ARG A 321 " --> pdb=" O   TYR A 317 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LEU A 323 " --> pdb=" O   GLN A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 363
      removed outlier: 3.976A  pdb=" N   GLU A 363 " --> pdb=" O   ALA A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 389
    Processing helix  chain 'A' and resid 391 through 399
    Processing helix  chain 'A' and resid 404 through 412
      removed outlier: 3.630A  pdb=" N   LEU A 408 " --> pdb=" O   GLN A 404 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLU A 409 " --> pdb=" O   PRO A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 437
      removed outlier: 3.563A  pdb=" N   ARG A 429 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ARG A 430 " --> pdb=" O   LYS A 426 " (cutoff:3.500A)
      Proline residue:  A 433  - end of helix
    Processing helix  chain 'A' and resid 440 through 449
    Processing helix  chain 'A' and resid 474 through 495
    Processing helix  chain 'A' and resid 512 through 541
      removed outlier: 4.062A  pdb=" N   GLU A 539 " --> pdb=" O   ALA A 535 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   TYR A 540 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   PHE A 541 " --> pdb=" O   PHE A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 562
    Processing helix  chain 'A' and resid 591 through 596
    Processing helix  chain 'A' and resid 618 through 622
    Processing helix  chain 'A' and resid 629 through 640
      removed outlier: 4.163A  pdb=" N   PHE A 635 " --> pdb=" O   GLU A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 650
    Processing helix  chain 'A' and resid 660 through 667
    Processing helix  chain 'A' and resid 671 through 684
    Processing helix  chain 'A' and resid 700 through 711
    Processing helix  chain 'A' and resid 722 through 732
      removed outlier: 3.682A  pdb=" N   ASP A 726 " --> pdb=" O   HIS A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 750
      removed outlier: 3.727A  pdb=" N   MET A 750 " --> pdb=" O   ARG A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 778 through 789
      removed outlier: 3.761A  pdb=" N   GLU A 782 " --> pdb=" O   PHE A 778 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   MET A 784 " --> pdb=" O   ALA A 780 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 814
    Processing helix  chain 'A' and resid 817 through 821
      removed outlier: 4.130A  pdb=" N   VAL A 821 " --> pdb=" O   PRO A 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 873
      removed outlier: 3.934A  pdb=" N   GLU A 873 " --> pdb=" O   LEU A 869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 881 through 893
      removed outlier: 3.686A  pdb=" N   TYR A 885 " --> pdb=" O   GLU A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 898 through 903
    Processing helix  chain 'A' and resid 965 through 972
    Processing helix  chain 'A' and resid 984 through 988
    Processing helix  chain 'D' and resid 13 through 19
    Processing helix  chain 'D' and resid 20 through 23
    Processing helix  chain 'D' and resid 24 through 44
      Proline residue:  D  30  - end of helix
    Processing helix  chain 'D' and resid 46 through 51
      removed outlier: 4.118A  pdb=" N   LYS D  50 " --> pdb=" O   ARG D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 85
    Processing sheet with id=AA1, first strand: chain 'A' and resid 695 through 697
      removed outlier: 6.675A  pdb=" N   ILE A 501 " --> pdb=" O   PHE A 696 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ARG A 500 " --> pdb=" O   TYR A  11 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ASP A  40 " --> pdb=" O   MET A  26 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLU A  28 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   LEU A  38 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 268
      removed outlier: 3.922A  pdb=" N   ALA A 267 " --> pdb=" O   VAL A 421 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289
    Processing sheet with id=AA4, first strand: chain 'A' and resid 586 through 588
    Processing sheet with id=AA5, first strand: chain 'A' and resid 858 through 863
    Processing sheet with id=AA6, first strand: chain 'A' and resid 933 through 935
    Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 964
      removed outlier: 3.772A  pdb=" N   PHE A 999 " --> pdb=" O   VAL A 952 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   GLU A 954 " --> pdb=" O   PHE A 997 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   PHE A 997 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 977 through 978
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1046 through 1050
      removed outlier: 3.664A  pdb=" N   ILE A1032 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   GLY A1049 " --> pdb=" O   ILE A1030 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ILE A1030 " --> pdb=" O   GLY A1049 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   SER A1022 " --> pdb=" O   ASN A1031 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   ARG A1033 " --> pdb=" O   PHE A1020 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   PHE A1020 " --> pdb=" O   ARG A1033 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASP A1005 " --> pdb=" O   PHE A1020 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LEU A1006 " --> pdb=" O   TYR A1061 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER A1057 " --> pdb=" O   ILE A1010 " (cutoff:3.500A)

    375 hydrogen bonds defined for protein.
    1075 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      86 hydrogen bonds
      160 hydrogen bond angles
      0 basepair planarities
      35 basepair parallelities
      62 stacking parallelities
  Total time for adding SS restraints: 2.19

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3324
        1.34 -     1.46: 2893
        1.46 -     1.58: 5251
        1.58 -     1.70: 228
        1.70 -     1.82: 43
  Bond restraints: 11739
  Sorted by residual:
  bond pdb=" CA  LYS A 269 "
       pdb=" CB  LYS A 269 "
    ideal  model  delta    sigma   weight residual
    1.524  1.543 -0.019 1.31e-02 5.83e+03 2.19e+00
  bond pdb=" C3'   G B  43 "
       pdb=" O3'   G B  43 "
    ideal  model  delta    sigma   weight residual
    1.415  1.439 -0.024 2.00e-02 2.50e+03 1.42e+00
  bond pdb=" N  AARG A 538 "
       pdb=" CA AARG A 538 "
    ideal  model  delta    sigma   weight residual
    1.458  1.474 -0.017 1.42e-02 4.96e+03 1.38e+00
  bond pdb=" N  BARG A 538 "
       pdb=" CA BARG A 538 "
    ideal  model  delta    sigma   weight residual
    1.458  1.474 -0.017 1.42e-02 4.96e+03 1.38e+00
  bond pdb=" C3'   A B  77 "
       pdb=" O3'   A B  77 "
    ideal  model  delta    sigma   weight residual
    1.415  1.438 -0.023 2.00e-02 2.50e+03 1.36e+00
  ... (remaining 11734 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 15947
        2.36 -     4.72: 393
        4.72 -     7.09: 36
        7.09 -     9.45: 2
        9.45 -    11.81: 2
  Bond angle restraints: 16380
  Sorted by residual:
  angle pdb=" C3'   A B  77 "
        pdb=" O3'   A B  77 "
        pdb=" P     A B  78 "
      ideal   model   delta    sigma   weight residual
     119.70  125.05   -5.35 1.20e+00 6.94e-01 1.99e+01
  angle pdb=" C   PRO A 309 "
        pdb=" N   TYR A 310 "
        pdb=" CA  TYR A 310 "
      ideal   model   delta    sigma   weight residual
     121.54  129.29   -7.75 1.91e+00 2.74e-01 1.65e+01
  angle pdb=" CB  MET A 350 "
        pdb=" CG  MET A 350 "
        pdb=" SD  MET A 350 "
      ideal   model   delta    sigma   weight residual
     112.70  124.51  -11.81 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" N   LYS A 269 "
        pdb=" CA  LYS A 269 "
        pdb=" C   LYS A 269 "
      ideal   model   delta    sigma   weight residual
     111.81  106.41    5.40 1.44e+00 4.82e-01 1.41e+01
  angle pdb=" C3'   G B  43 "
        pdb=" O3'   G B  43 "
        pdb=" P     A B  44 "
      ideal   model   delta    sigma   weight residual
     119.70  123.90   -4.20 1.20e+00 6.94e-01 1.23e+01
  ... (remaining 16375 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.96: 5822
       19.96 -    39.92: 737
       39.92 -    59.88: 301
       59.88 -    79.84: 52
       79.84 -    99.80: 7
  Dihedral angle restraints: 6919
    sinusoidal: 3669
      harmonic: 3250
  Sorted by residual:
  dihedral pdb=" C4'   A B  77 "
           pdb=" C3'   A B  77 "
           pdb=" C2'   A B  77 "
           pdb=" C1'   A B  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -37.42   73.77     1      3.10e+00 1.04e-01 7.20e+02
  dihedral pdb=" C4'   A B  44 "
           pdb=" C3'   A B  44 "
           pdb=" C2'   A B  44 "
           pdb=" C1'   A B  44 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.06   73.41     1      3.10e+00 1.04e-01 7.14e+02
  dihedral pdb=" C4'   G B  43 "
           pdb=" C3'   G B  43 "
           pdb=" C2'   G B  43 "
           pdb=" C1'   G B  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.34   72.69     1      3.10e+00 1.04e-01 7.02e+02
  ... (remaining 6916 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 1693
       0.085 -    0.170: 68
       0.170 -    0.256: 122
       0.256 -    0.341: 17
       0.341 -    0.426: 1
  Chirality restraints: 1901
  Sorted by residual:
  chirality pdb=" P     A B  78 "
            pdb=" OP1   A B  78 "
            pdb=" OP2   A B  78 "
            pdb=" O5'   A B  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.60   -0.43 2.00e-01 2.50e+01 4.54e+00
  chirality pdb=" P     A B  45 "
            pdb=" OP1   A B  45 "
            pdb=" OP2   A B  45 "
            pdb=" O5'   A B  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.50   -0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" P     A B  44 "
            pdb=" OP1   A B  44 "
            pdb=" OP2   A B  44 "
            pdb=" O5'   A B  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.46   -0.29 2.00e-01 2.50e+01 2.05e+00
  ... (remaining 1898 not shown)

  Planarity restraints: 1707
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 123 "   -0.032 5.00e-02 4.00e+02   4.93e-02 3.88e+00
        pdb=" N   PRO A 124 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 124 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 124 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 109 "   -0.032 5.00e-02 4.00e+02   4.85e-02 3.76e+00
        pdb=" N   PRO A 110 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 110 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 110 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 580 "    0.009 2.00e-02 2.50e+03   1.86e-02 3.48e+00
        pdb=" C   GLU A 580 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   GLU A 580 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LYS A 581 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1704 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 767
        2.73 -     3.27: 10703
        3.27 -     3.81: 18933
        3.81 -     4.36: 22219
        4.36 -     4.90: 35720
  Nonbonded interactions: 88342
  Sorted by model distance:
  nonbonded pdb=" O   THR A 237 "
            pdb=" OG1 THR A 241 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" O   GLN A 919 "
            pdb=" O2'   U B  56 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" NZ  LYS A 390 "
            pdb=" O   PHE A 417 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OE2 GLU A 261 "
            pdb=" OH  TYR A 449 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O2'   A B  17 "
            pdb=" O4    U B 132 "
     model   vdw
     2.245 3.040
  ... (remaining 88337 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.810
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11739  Z= 0.120
  Angle     :  0.704  11.811  16380  Z= 0.322
  Chirality :  0.074   0.426   1901
  Planarity :  0.004   0.049   1707
  Dihedral  : 19.583  99.802   4811
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  5.64 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 28.90 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.26), residues: 1107
  helix:  0.66 (0.25), residues: 465
  sheet: -0.17 (0.54), residues: 104
  loop : -1.53 (0.26), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 646 
 TYR   0.012   0.001   TYR A 317 
 PHE   0.024   0.001   PHE D   8 
 TRP   0.016   0.001   TRP A 632 
 HIS   0.002   0.000   HIS A 843 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.12 (11739)
  covalent geometry    : angle       0.70351 /  0.32 (16380)
  hydrogen bonds       : bond        0.14472 / 10.05 (  461)
  hydrogen bonds       : angle       4.98538 /  3.78 ( 1235)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.348 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1007
  time to fit residues: 15.2299
Evaluate side-chains
  91 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    9.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    4.4788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 611 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.144669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.115475 restraints weight = 48818.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.116136 restraints weight = 36604.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.118153 restraints weight = 22631.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.118309 restraints weight = 15385.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.120315 restraints weight = 13462.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3631
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3631 r_free = 0.3631    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3631 r_free = 0.3631    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3631
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067  11739  Z= 0.310
  Angle     :  1.056  18.067  16380  Z= 0.455
  Chirality :  0.075   0.805   1901
  Planarity :  0.006   0.051   1707
  Dihedral  : 15.276 157.551   2600
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  7.55 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 28.46 %
    Favored  : 69.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.25), residues: 1107
  helix:  0.50 (0.24), residues: 466
  sheet: -0.60 (0.54), residues: 102
  loop : -1.74 (0.26), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 646 
 TYR   0.022   0.002   TYR A 317 
 PHE   0.045   0.002   PHE A 185 
 TRP   0.012   0.002   TRP A 111 
 HIS   0.005   0.002   HIS D  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00702 /  0.31 (11739)
  covalent geometry    : angle       1.05634 /  0.46 (16380)
  hydrogen bonds       : bond        0.06736 /  4.70 (  461)
  hydrogen bonds       : angle       4.48391 /  3.28 ( 1235)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  246 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7747 (mt)
  outliers start: 23
  outliers final: 10
  residues processed: 101
  average time/residue: 0.0897
  time to fit residues: 13.3719
Evaluate side-chains
  90 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  505 THR
Chi-restraints excluded: chain A residue  526 ASN
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain D residue   10 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   chunk 113 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 106 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9980
   chunk 119 optimal weight:   10.0000
   overall best weight:    1.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 822 HIS
A 944 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.145329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.114198 restraints weight = 57101.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.115217 restraints weight = 31316.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.116577 restraints weight = 20341.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.117113 restraints weight = 13721.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.118587 restraints weight = 12324.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3559 r_free = 0.3559    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3558 r_free = 0.3558    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11739  Z= 0.162
  Angle     :  0.836  12.491  16380  Z= 0.364
  Chirality :  0.061   0.642   1901
  Planarity :  0.004   0.049   1707
  Dihedral  : 15.259 153.077   2600
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  6.55 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 28.14 %
    Favored  : 69.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.25), residues: 1107
  helix:  0.82 (0.25), residues: 465
  sheet: -0.58 (0.53), residues: 102
  loop : -1.63 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 713 
 TYR   0.017   0.001   TYR A 317 
 PHE   0.027   0.001   PHE A 185 
 TRP   0.009   0.001   TRP A 632 
 HIS   0.002   0.001   HIS A 414 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.16 (11739)
  covalent geometry    : angle       0.83579 /  0.36 (16380)
  hydrogen bonds       : bond        0.04841 /  3.37 (  461)
  hydrogen bonds       : angle       4.07755 /  2.99 ( 1235)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  246 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7807 (mt)
REVERT: A  501 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8192 (mp)
REVERT: A  580 GLU cc_start: 0.6435 (tm-30) cc_final: 0.6196 (tm-30)
  outliers start: 22
  outliers final: 11
  residues processed: 101
  average time/residue: 0.0890
  time to fit residues: 13.2498
Evaluate side-chains
  95 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain D residue   10 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 88 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0570
   chunk 90 optimal weight:    2.9990
   chunk 92 optimal weight:    0.0370
   chunk 51 optimal weight:    0.8980
   chunk 114 optimal weight:    5.9990
   chunk 120 optimal weight:    7.9990
   chunk 103 optimal weight:    9.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.3980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.146844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.115997 restraints weight = 58523.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.119185 restraints weight = 32717.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.119534 restraints weight = 18385.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.120288 restraints weight = 12339.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.120642 restraints weight = 11126.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3591
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3591
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11739  Z= 0.142
  Angle     :  0.794  11.330  16380  Z= 0.347
  Chirality :  0.057   0.487   1901
  Planarity :  0.004   0.051   1707
  Dihedral  : 15.059 151.063   2600
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  6.45 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 27.81 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.26), residues: 1107
  helix:  0.99 (0.25), residues: 465
  sheet: -0.49 (0.52), residues: 101
  loop : -1.56 (0.26), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 713 
 TYR   0.016   0.001   TYR A 317 
 PHE   0.025   0.001   PHE A 185 
 TRP   0.010   0.001   TRP A 632 
 HIS   0.003   0.001   HIS A1002 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.14 (11739)
  covalent geometry    : angle       0.79411 /  0.35 (16380)
  hydrogen bonds       : bond        0.04553 /  3.17 (  461)
  hydrogen bonds       : angle       3.92616 /  2.88 ( 1235)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  246 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7978 (mt)
REVERT: A  249 ASP cc_start: 0.7529 (m-30) cc_final: 0.7303 (m-30)
REVERT: A  276 ARG cc_start: 0.7454 (tpt170) cc_final: 0.7200 (tpt170)
REVERT: A  501 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8235 (mt)
  outliers start: 23
  outliers final: 15
  residues processed: 106
  average time/residue: 0.0950
  time to fit residues: 14.8500
Evaluate side-chains
  100 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain D residue   79 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 69 optimal weight:    7.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.141365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.110939 restraints weight = 45799.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.112706 restraints weight = 26559.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.113080 restraints weight = 18484.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.114338 restraints weight = 12015.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.114598 restraints weight = 10480.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3508
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3508
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  11739  Z= 0.275
  Angle     :  0.924  11.930  16380  Z= 0.407
  Chirality :  0.065   0.540   1901
  Planarity :  0.006   0.051   1707
  Dihedral  : 15.149 150.639   2600
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  7.64 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 28.14 %
    Favored  : 69.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.25), residues: 1107
  helix:  0.54 (0.25), residues: 467
  sheet: -0.82 (0.53), residues: 99
  loop : -1.78 (0.25), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 713 
 TYR   0.023   0.002   TYR A 317 
 PHE   0.031   0.002   PHE A 185 
 TRP   0.013   0.002   TRP A 111 
 HIS   0.005   0.001   HIS A 133 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00630 /  0.28 (11739)
  covalent geometry    : angle       0.92415 /  0.41 (16380)
  hydrogen bonds       : bond        0.06294 /  4.37 (  461)
  hydrogen bonds       : angle       4.37017 /  3.20 ( 1235)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  118 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6786 (mt)
REVERT: A  246 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7954 (mt)
REVERT: A  276 ARG cc_start: 0.7589 (tpt170) cc_final: 0.7271 (tpt170)
  outliers start: 24
  outliers final: 16
  residues processed: 101
  average time/residue: 0.0916
  time to fit residues: 13.7195
Evaluate side-chains
  99 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   47 ASP
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   79 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 83 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0020
   chunk 21 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   overall best weight:    1.9996

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.141503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.108933 restraints weight = 75646.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.112577 restraints weight = 34362.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.112688 restraints weight = 17258.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.114118 restraints weight = 11412.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.114651 restraints weight = 9694.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11739  Z= 0.165
  Angle     :  0.813  10.251  16380  Z= 0.356
  Chirality :  0.059   0.448   1901
  Planarity :  0.004   0.051   1707
  Dihedral  : 15.081 154.215   2600
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  6.91 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 28.79 %
    Favored  : 68.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.26), residues: 1107
  helix:  0.79 (0.25), residues: 468
  sheet: -0.83 (0.53), residues: 104
  loop : -1.64 (0.26), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 713 
 TYR   0.020   0.001   TYR A 317 
 PHE   0.022   0.001   PHE D   8 
 TRP   0.011   0.001   TRP A 632 
 HIS   0.003   0.001   HIS A 822 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.17 (11739)
  covalent geometry    : angle       0.81291 /  0.36 (16380)
  hydrogen bonds       : bond        0.04981 /  3.48 (  461)
  hydrogen bonds       : angle       4.06359 /  2.98 ( 1235)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   86 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6509 (tp)
REVERT: A  246 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8016 (mt)
REVERT: A  402 ARG cc_start: 0.6665 (mtt-85) cc_final: 0.6146 (mtt90)
REVERT: A  801 ASP cc_start: 0.7661 (p0) cc_final: 0.7340 (p0)
  outliers start: 26
  outliers final: 18
  residues processed: 106
  average time/residue: 0.0965
  time to fit residues: 14.9550
Evaluate side-chains
  104 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   79 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 59 optimal weight:    9.9990
   chunk 89 optimal weight:    6.9990
   chunk 49 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    3.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 422 GLN
A 611 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.141690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.110678 restraints weight = 60275.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.111990 restraints weight = 34323.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.113435 restraints weight = 19831.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.114093 restraints weight = 13049.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.114634 restraints weight = 11763.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3502
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3502 r_free = 0.3502    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3502
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  11739  Z= 0.257
  Angle     :  0.896   9.887  16380  Z= 0.395
  Chirality :  0.064   0.502   1901
  Planarity :  0.005   0.050   1707
  Dihedral  : 15.109 169.758   2600
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  8.00 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 28.57 %
    Favored  : 68.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.99 (0.25), residues: 1107
  helix:  0.58 (0.25), residues: 467
  sheet: -0.90 (0.54), residues: 99
  loop : -1.76 (0.26), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 713 
 TYR   0.023   0.002   TYR A 317 
 PHE   0.027   0.002   PHE A 185 
 TRP   0.012   0.002   TRP A 632 
 HIS   0.004   0.001   HIS A 822 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00586 /  0.26 (11739)
  covalent geometry    : angle       0.89647 /  0.39 (16380)
  hydrogen bonds       : bond        0.05990 /  4.16 (  461)
  hydrogen bonds       : angle       4.30325 /  3.16 ( 1235)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A   86 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6515 (tp)
REVERT: A  246 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8095 (mt)
REVERT: A  801 ASP cc_start: 0.7574 (p0) cc_final: 0.7369 (p0)
REVERT: A  819 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6929 (mp0)
  outliers start: 28
  outliers final: 17
  residues processed: 109
  average time/residue: 0.1014
  time to fit residues: 16.0385
Evaluate side-chains
  104 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  819 GLU
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   79 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 93 optimal weight:    0.4980
   chunk 61 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 37 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 30 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   chunk 83 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   overall best weight:    2.8986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.142811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.110967 restraints weight = 58361.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.113894 restraints weight = 28982.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.114388 restraints weight = 16543.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.114700 restraints weight = 11713.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.115162 restraints weight = 10983.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3512
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3512
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  11739  Z= 0.208
  Angle     :  0.852   9.590  16380  Z= 0.374
  Chirality :  0.061   0.459   1901
  Planarity :  0.005   0.050   1707
  Dihedral  : 15.057 174.280   2600
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  7.36 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 28.79 %
    Favored  : 68.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.25), residues: 1107
  helix:  0.64 (0.25), residues: 468
  sheet: -0.87 (0.54), residues: 99
  loop : -1.72 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 713 
 TYR   0.022   0.002   TYR A 317 
 PHE   0.031   0.002   PHE D   8 
 TRP   0.013   0.001   TRP A 632 
 HIS   0.003   0.001   HIS A1002 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00473 /  0.21 (11739)
  covalent geometry    : angle       0.85190 /  0.37 (16380)
  hydrogen bonds       : bond        0.05406 /  3.76 (  461)
  hydrogen bonds       : angle       4.16385 /  3.05 ( 1235)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   86 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6486 (tp)
REVERT: A  246 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8062 (mt)
REVERT: A  801 ASP cc_start: 0.7621 (p0) cc_final: 0.7416 (p0)
REVERT: A  819 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6925 (mp0)
  outliers start: 25
  outliers final: 20
  residues processed: 103
  average time/residue: 0.0923
  time to fit residues: 13.9654
Evaluate side-chains
  104 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   56 ASP
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  216 PHE
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  526 ASN
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  819 GLU
Chi-restraints excluded: chain A residue  948 VAL
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1037 LEU
Chi-restraints excluded: chain A residue 1052 VAL
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   79 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 102 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 103 optimal weight:    0.6980
   chunk 8 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0970
   chunk 33 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.7378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 562 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.145083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.111872 restraints weight = 49946.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.113706 restraints weight = 23209.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.114486 restraints weight = 14205.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.115324 restraints weight = 10100.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.115979 restraints weight = 9097.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3526
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3526
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
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   0.045  11739  Z= 0.121
  Angle     :  0.761   9.789  16380  Z= 0.333
  Chirality :  0.056   0.470   1901
  Planarity :  0.004   0.051   1707
  Dihedral  : 14.797 154.214   2600
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  6.18 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 29.12 %
    Favored  : 68.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.26), residues: 1107
  helix:  1.03 (0.25), residues: 466
  sheet: -0.60 (0.52), residues: 106
  loop : -1.48 (0.26), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 713 
 TYR   0.018   0.001   TYR A 317 
 PHE   0.025   0.001   PHE D   8 
 TRP   0.011   0.001   TRP A 632 
 HIS   0.002   0.000   HIS A1002 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 (11739)
  covalent geometry    : angle       0.76149 /  0.33 (16380)
  hydrogen bonds       : bond        0.04133 /  2.90 (  461)
  hydrogen bonds       : angle       3.82974 /  2.79 ( 1235)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  246 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8109 (mt)
REVERT: A  348 MET cc_start: 0.7319 (tmm) cc_final: 0.7085 (tmm)
REVERT: A  402 ARG cc_start: 0.6672 (mtt-85) cc_final: 0.6358 (mtt90)
REVERT: A  620 TYR cc_start: 0.8110 (t80) cc_final: 0.7757 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 111
  average time/residue: 0.0850
  time to fit residues: 13.9671
Evaluate side-chains
  97 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  660 ASP
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   22 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 26 optimal weight:   20.0000
   chunk 0 optimal weight:    8.9990
   chunk 105 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 72 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0030
   chunk 56 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   overall best weight:    2.5596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.141127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.106775 restraints weight = 63021.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.112643 restraints weight = 25404.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.111649 restraints weight = 13730.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.111856 restraints weight = 9992.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.112380 restraints weight = 8994.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  11739  Z= 0.192
  Angle     :  0.820   8.937  16380  Z= 0.362
  Chirality :  0.059   0.423   1901
  Planarity :  0.005   0.052   1707
  Dihedral  : 14.743 142.936   2600
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  7.18 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 29.99 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.26), residues: 1107
  helix:  0.87 (0.25), residues: 473
  sheet: -0.72 (0.53), residues: 98
  loop : -1.68 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 713 
 TYR   0.020   0.001   TYR A 317 
 PHE   0.025   0.002   PHE D   8 
 TRP   0.026   0.002   TRP A 632 
 HIS   0.003   0.001   HIS A1002 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00438 /  0.19 (11739)
  covalent geometry    : angle       0.82032 /  0.36 (16380)
  hydrogen bonds       : bond        0.05136 /  3.57 (  461)
  hydrogen bonds       : angle       4.03408 /  2.95 ( 1235)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A   86 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6531 (tp)
REVERT: A  246 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8137 (mt)
REVERT: A  620 TYR cc_start: 0.8172 (t80) cc_final: 0.7904 (t80)
  outliers start: 16
  outliers final: 14
  residues processed: 97
  average time/residue: 0.0915
  time to fit residues: 13.4864
Evaluate side-chains
  98 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 SER
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  216 PHE
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  310 TYR
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  526 ASN
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  660 ASP
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain D residue   10 THR
Chi-restraints excluded: chain D residue   58 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 112 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 44 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0030
   chunk 28 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0670
   chunk 80 optimal weight:    0.3980
   chunk 81 optimal weight:    0.3980
   overall best weight:    0.3128

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 474 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.146910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.114006 restraints weight = 61555.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.118001 restraints weight = 25503.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.118334 restraints weight = 12777.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.118469 restraints weight = 10205.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.119019 restraints weight = 9144.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11739  Z= 0.118
  Angle     :  0.752   9.415  16380  Z= 0.331
  Chirality :  0.055   0.441   1901
  Planarity :  0.004   0.052   1707
  Dihedral  : 14.675 144.308   2600
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.55 %
    Allowed  :  5.82 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 30.21 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.26), residues: 1107
  helix:  1.14 (0.25), residues: 470
  sheet: -0.40 (0.53), residues: 106
  loop : -1.43 (0.27), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 713 
 TYR   0.014   0.001   TYR A 317 
 PHE   0.020   0.001   PHE D   8 
 TRP   0.018   0.002   TRP A 632 
 HIS   0.002   0.000   HIS A 354 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 (11739)
  covalent geometry    : angle       0.75159 /  0.33 (16380)
  hydrogen bonds       : bond        0.04055 /  2.85 (  461)
  hydrogen bonds       : angle       3.82254 /  2.79 ( 1235)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1774.65 seconds
wall clock time: 31 minutes 22.13 seconds (1882.13 seconds total)