Starting phenix.real_space_refine
on Fri Aug 22 18:50:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u4v_41899/08_2025/8u4v_41899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u4v_41899/08_2025/8u4v_41899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u4v_41899/08_2025/8u4v_41899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u4v_41899/08_2025/8u4v_41899.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u4v_41899/08_2025/8u4v_41899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u4v_41899/08_2025/8u4v_41899.map"
  }
  resolution = 2.99
  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=   0.000 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    4212      2.51       5
     N    1102      2.21       5
     O    1292      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6637
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1324
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1324
          Classifications: {'peptide': 180}
          Link IDs: {'PTRANS': 4, 'TRANS': 175}
    Chain: "B"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 970
          Classifications: {'peptide': 122}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 1620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1620
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202}
    Chain: "H"
      Number of atoms: 1735
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 228, 1724
          Classifications: {'peptide': 228}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215}
      Conformer: "B"
        Number of residues, atoms: 228, 1724
          Classifications: {'peptide': 228}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215}
          bond proxies already assigned to first conformer: 1761
    Chain: "K"
      Number of atoms: 916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 916
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "H"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 69
          Unusual residues: {'AV0': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 2.30, per 1000 atoms: 0.35
  Number of scatterers: 6637
  At special positions: 0
  Unit cell: (77.964, 96.12, 129.228, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1292      8.00
     N    1102      7.00
     C    4212      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  64 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  48 " - pdb=" SG  CYS L 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 159 " - pdb=" SG  CYS L 219 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  48 " - pdb=" SG  CYS H 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 180 " - pdb=" SG  CYS H 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " distance=2.04

  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: 0.53
  Conformation dependent library (CDL) restraints added in 418.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1588

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 17 sheets defined
      20.6% alpha, 38.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 27
    Processing helix  chain 'A' and resid 69 through 73
      removed outlier: 3.600A  pdb=" N   LEU A  73 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 101
      removed outlier: 3.602A  pdb=" N   ALA A  79 " --> pdb=" O   GLN A  75 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ALA A  80 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 149
      Proline residue:  A 135  - end of helix
    Processing helix  chain 'A' and resid 161 through 183
      removed outlier: 3.734A  pdb=" N   TYR A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 217
    Processing helix  chain 'B' and resid 267 through 270
      removed outlier: 3.666A  pdb=" N   ASN B 270 " --> pdb=" O   ASN B 267 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 267 through 270'
    Processing helix  chain 'L' and resid 104 through 108
      removed outlier: 4.109A  pdb=" N   PHE L 108 " --> pdb=" O   PRO L 105 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 146 through 153
    Processing helix  chain 'L' and resid 208 through 212
    Processing helix  chain 'H' and resid 54 through 57
      removed outlier: 3.636A  pdb=" N   SER H  57 " --> pdb=" O   ASN H  54 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 54 through 57'
    Processing helix  chain 'H' and resid 113 through 117
    Processing helix  chain 'H' and resid 130 through 137
      removed outlier: 3.588A  pdb=" N   LEU H 135 " --> pdb=" O   TRP H 131 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 196 through 198
      No H-bonds generated for 'chain 'H' and resid 196 through 198'
    Processing helix  chain 'H' and resid 225 through 229
      removed outlier: 3.531A  pdb=" N   LEU H 229 " --> pdb=" O   SER H 226 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 53 through 57
      removed outlier: 4.147A  pdb=" N   GLY K  57 " --> pdb=" O   SER K  54 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66
    Processing sheet with id=AA2, first strand: chain 'B' and resid 205 through 210
      removed outlier: 7.133A  pdb=" N   ALA B 205 " --> pdb=" O   ASN B 239 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   HIS B 241 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   GLU B 207 " --> pdb=" O   HIS B 241 " (cutoff:3.500A)
      removed outlier: 8.285A  pdb=" N   THR B 243 " --> pdb=" O   GLU B 207 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   LEU B 209 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   SER B 265 " --> pdb=" O   LYS B 273 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   LYS B 273 " --> pdb=" O   SER B 265 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 223 through 227
      removed outlier: 3.912A  pdb=" N   GLN B 249 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   HIS B 285 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 29 through 32
    Processing sheet with id=AA5, first strand: chain 'L' and resid 35 through 38
      removed outlier: 6.113A  pdb=" N   GLN L  62 " --> pdb=" O   LEU L  71 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   LEU L  71 " --> pdb=" O   GLN L  62 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 35 through 38
    Processing sheet with id=AA7, first strand: chain 'L' and resid 139 through 143
      removed outlier: 5.495A  pdb=" N   TYR L 198 " --> pdb=" O   ASN L 163 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 169 through 174
    Processing sheet with id=AA9, first strand: chain 'H' and resid 29 through 33
    Processing sheet with id=AB1, first strand: chain 'H' and resid 37 through 38
      removed outlier: 4.214A  pdb=" N   TRP H 125 " --> pdb=" O   TYR H  59 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   TYR H  59 " --> pdb=" O   TRP H 125 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   ARG H  64 " --> pdb=" O   TRP H  73 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   TRP H  73 " --> pdb=" O   ARG H  64 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 37 through 38
    Processing sheet with id=AB3, first strand: chain 'H' and resid 161 through 164
      removed outlier: 3.584A  pdb=" N   SER H 220 " --> pdb=" O   CYS H 180 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ASP H 184 " --> pdb=" O   TYR H 216 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   TYR H 216 " --> pdb=" O   ASP H 184 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 161 through 164
      removed outlier: 3.584A  pdb=" N   SER H 220 " --> pdb=" O   CYS H 180 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ASP H 184 " --> pdb=" O   TYR H 216 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   TYR H 216 " --> pdb=" O   ASP H 184 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 191 through 194
      removed outlier: 4.792A  pdb=" N   TYR H 234 " --> pdb=" O   VAL H 251 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'K' and resid 3 through 6
      removed outlier: 6.055A  pdb=" N   GLY K  16 " --> pdb=" O   SER K  85 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'K' and resid 59 through 60
      removed outlier: 5.532A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA K  33 " --> pdb=" O   ASP K  99 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'K' and resid 92 through 93

    335 hydrogen bonds defined for protein.
    891 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1464
        1.33 -     1.45: 1560
        1.45 -     1.57: 3717
        1.57 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 6785
  Sorted by residual:
  bond pdb=" N   GLY K  10 "
       pdb=" CA  GLY K  10 "
    ideal  model  delta    sigma   weight residual
    1.448  1.477 -0.029 9.20e-03 1.18e+04 9.94e+00
  bond pdb=" N   VAL K  50 "
       pdb=" CA  VAL K  50 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.15e-02 7.56e+03 9.27e+00
  bond pdb=" CCJ AV0 H 301 "
       pdb=" OBV AV0 H 301 "
    ideal  model  delta    sigma   weight residual
    1.374  1.431 -0.057 2.00e-02 2.50e+03 8.11e+00
  bond pdb=" CA  SER L  35 "
       pdb=" CB  SER L  35 "
    ideal  model  delta    sigma   weight residual
    1.533  1.489  0.044 1.66e-02 3.63e+03 7.10e+00
  bond pdb=" N   ILE K  29 "
       pdb=" CA  ILE K  29 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.35e-02 5.49e+03 7.09e+00
  ... (remaining 6780 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.71: 9215
        6.71 -    13.42: 9
       13.42 -    20.13: 2
       20.13 -    26.84: 3
       26.84 -    33.55: 2
  Bond angle restraints: 9231
  Sorted by residual:
  angle pdb=" CBR AV0 H 301 "
        pdb=" CCM AV0 H 301 "
        pdb=" CBT AV0 H 301 "
      ideal   model   delta    sigma   weight residual
     110.70   77.15   33.55 3.00e+00 1.11e-01 1.25e+02
  angle pdb=" CBQ AV0 H 301 "
        pdb=" CCM AV0 H 301 "
        pdb=" CBS AV0 H 301 "
      ideal   model   delta    sigma   weight residual
     110.52   81.56   28.96 3.00e+00 1.11e-01 9.32e+01
  angle pdb=" C   ARG K  38 "
        pdb=" CA  ARG K  38 "
        pdb=" CB  ARG K  38 "
      ideal   model   delta    sigma   weight residual
     109.38   92.93   16.45 1.80e+00 3.09e-01 8.35e+01
  angle pdb=" CBQ AV0 H 301 "
        pdb=" CCM AV0 H 301 "
        pdb=" CBR AV0 H 301 "
      ideal   model   delta    sigma   weight residual
     107.79   81.90   25.89 3.00e+00 1.11e-01 7.45e+01
  angle pdb=" CBS AV0 H 301 "
        pdb=" CCM AV0 H 301 "
        pdb=" CBT AV0 H 301 "
      ideal   model   delta    sigma   weight residual
     105.72   80.28   25.44 3.00e+00 1.11e-01 7.19e+01
  ... (remaining 9226 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.10: 3780
       23.10 -    46.19: 246
       46.19 -    69.29: 48
       69.29 -    92.38: 7
       92.38 -   115.48: 8
  Dihedral angle restraints: 4089
    sinusoidal: 1603
      harmonic: 2486
  Sorted by residual:
  dihedral pdb=" C   ARG K  38 "
           pdb=" N   ARG K  38 "
           pdb=" CA  ARG K  38 "
           pdb=" CB  ARG K  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -101.94  -20.66     0      2.50e+00 1.60e-01 6.83e+01
  dihedral pdb=" CB  CYS H 180 "
           pdb=" SG  CYS H 180 "
           pdb=" SG  CYS H 236 "
           pdb=" CB  CYS H 236 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -132.12   46.12     1      1.00e+01 1.00e-02 2.95e+01
  dihedral pdb=" C   ASN L 163 "
           pdb=" N   ASN L 163 "
           pdb=" CA  ASN L 163 "
           pdb=" CB  ASN L 163 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.49   11.89     0      2.50e+00 1.60e-01 2.26e+01
  ... (remaining 4086 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 985
       0.111 -    0.222: 65
       0.222 -    0.332: 4
       0.332 -    0.443: 1
       0.443 -    0.554: 1
  Chirality restraints: 1056
  Sorted by residual:
  chirality pdb=" CA  ASN L 163 "
            pdb=" N   ASN L 163 "
            pdb=" C   ASN L 163 "
            pdb=" CB  ASN L 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.67e+00
  chirality pdb=" CA  ARG K  38 "
            pdb=" N   ARG K  38 "
            pdb=" C   ARG K  38 "
            pdb=" CB  ARG K  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.37 2.00e-01 2.50e+01 3.44e+00
  chirality pdb=" CA  LYS A 157 "
            pdb=" N   LYS A 157 "
            pdb=" C   LYS A 157 "
            pdb=" CB  LYS A 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.72e+00
  ... (remaining 1053 not shown)

  Planarity restraints: 1153
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  73 "   -0.039 5.00e-02 4.00e+02   5.99e-02 5.73e+00
        pdb=" N   PRO A  74 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A  74 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A  74 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 111 "    0.009 2.00e-02 2.50e+03   1.88e-02 3.52e+00
        pdb=" CD  GLU A 111 "   -0.032 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 111 "    0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 111 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER L 184 "   -0.008 2.00e-02 2.50e+03   1.57e-02 2.48e+00
        pdb=" C   SER L 184 "    0.027 2.00e-02 2.50e+03
        pdb=" O   SER L 184 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLN L 185 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1150 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 108
        2.63 -     3.20: 5758
        3.20 -     3.77: 10273
        3.77 -     4.33: 14642
        4.33 -     4.90: 24696
  Nonbonded interactions: 55477
  Sorted by model distance:
  nonbonded pdb=" O   THR H 171 "
            pdb=" OG1 THR H 175 "
     model   vdw
     2.063 3.040
  nonbonded pdb=" OG  SER L  51 "
            pdb=" OE1 GLN L  52 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   ALA L 178 "
            pdb=" NE2 GLN L 180 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" CBS AV0 H 301 "
            pdb=" OBV AV0 H 301 "
     model   vdw
     2.334 2.752
  nonbonded pdb=" O   SER L 119 "
            pdb=" OG  SER H  85 "
     model   vdw
     2.354 3.040
  ... (remaining 55472 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=0.47 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.480
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
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      :  0.006   0.057   6791  Z= 0.377
  Angle     :  1.120  33.548   9243  Z= 0.618
  Chirality :  0.060   0.554   1056
  Planarity :  0.004   0.060   1153
  Dihedral  : 16.562 115.481   2483
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 21.47 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.30), residues: 853
  helix:  2.16 (0.43), residues: 139
  sheet:  0.22 (0.29), residues: 344
  loop :  0.13 (0.35), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  53 
 TYR   0.007   0.001   TYR H 121 
 PHE   0.013   0.001   PHE K  37 
 TRP   0.015   0.001   TRP A  18 
 HIS   0.001   0.000   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 ( 6785)
  covalent geometry    : angle       1.12051 ( 9231)
  SS BOND              : bond        0.00204 (    6)
  SS BOND              : angle       0.94701 (   12)
  hydrogen bonds       : bond        0.17811 (  314)
  hydrogen bonds       : angle       7.61977 (  891)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 145
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A   52 MET cc_start: 0.8997 (ptp) cc_final: 0.8581 (ptt)
REVERT: A   78 GLN cc_start: 0.7249 (tt0) cc_final: 0.6797 (mt0)
REVERT: B  250 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7697 (tttp)
REVERT: L   49 ARG cc_start: 0.7848 (ttp-170) cc_final: 0.7058 (ttp-110)
REVERT: L  130 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7976 (mt-10)
REVERT: L  147 ASP cc_start: 0.8481 (p0) cc_final: 0.8261 (m-30)
REVERT: L  210 ASP cc_start: 0.8229 (t0) cc_final: 0.7545 (t0)
REVERT: H  250 LYS cc_start: 0.8816 (tttm) cc_final: 0.8561 (tptt)
REVERT: H  252 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8906 (mt-10)
REVERT: K   89 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7310 (pm20)
REVERT: K  101 ASP cc_start: 0.8254 (t0) cc_final: 0.7948 (t0)
  outliers start: 6
  outliers final: 1
  residues processed: 149
  average time/residue: 0.5879
  time to fit residues: 91.6516
Evaluate side-chains
  114 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain K residue   89 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 295 GLN
L 115 GLN
** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 185 GLN
H 211 GLN
K   3 GLN
K  77 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.090066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.067208 restraints weight = 16822.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 2.60
r_work: 0.2595 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2454 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2461
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2461 r_free = 0.2461    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2461 r_free = 0.2461    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2461
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6791  Z= 0.172
  Angle     :  0.905  31.819   9243  Z= 0.381
  Chirality :  0.043   0.171   1056
  Planarity :  0.004   0.053   1153
  Dihedral  :  8.801  87.854   1056
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 19.94 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.30), residues: 853
  helix:  2.37 (0.43), residues: 141
  sheet:  0.57 (0.29), residues: 350
  loop :  0.36 (0.36), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  72 
 TYR   0.012   0.001   TYR B 264 
 PHE   0.012   0.001   PHE B 261 
 TRP   0.011   0.001   TRP A  18 
 HIS   0.003   0.001   HIS H  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6785)
  covalent geometry    : angle       0.90487 ( 9231)
  SS BOND              : bond        0.00210 (    6)
  SS BOND              : angle       1.20217 (   12)
  hydrogen bonds       : bond        0.04138 (  314)
  hydrogen bonds       : angle       5.49249 (  891)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   78 GLN cc_start: 0.8507 (tt0) cc_final: 0.8266 (mm-40)
REVERT: A  130 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8767 (mm)
REVERT: B  250 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8743 (tttp)
REVERT: B  295 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8454 (mm-40)
REVERT: L   49 ARG cc_start: 0.9038 (ttp-170) cc_final: 0.8553 (ttp-110)
REVERT: L   91 ARG cc_start: 0.9074 (ttt180) cc_final: 0.8846 (ttt180)
REVERT: L   95 ASP cc_start: 0.8918 (m-30) cc_final: 0.8310 (m-30)
REVERT: L  130 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8448 (mt-10)
REVERT: L  175 VAL cc_start: 0.9198 (m) cc_final: 0.8857 (t)
REVERT: L  210 ASP cc_start: 0.8646 (t0) cc_final: 0.8356 (t0)
REVERT: L  238 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6860 (mp0)
REVERT: H  178 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8772 (mp)
REVERT: H  239 ASN cc_start: 0.9288 (t0) cc_final: 0.8985 (t0)
REVERT: H  246 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8905 (mmmt)
REVERT: K   44 GLU cc_start: 0.8815 (pm20) cc_final: 0.8601 (pm20)
REVERT: K   89 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8182 (pm20)
  outliers start: 25
  outliers final: 7
  residues processed: 130
  average time/residue: 0.5143
  time to fit residues: 70.0863
Evaluate side-chains
  118 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  264 TYR
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue   34 SER
Chi-restraints excluded: chain L residue  238 GLU
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  246 LYS
Chi-restraints excluded: chain K residue   89 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 52 optimal weight:    0.4980
   chunk 17 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 69 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.089070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.065297 restraints weight = 22378.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.2683 rms_B_bonded: 3.01
r_work: 0.2544 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2544
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2553 r_free = 0.2553    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2553 r_free = 0.2553    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8822
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6791  Z= 0.172
  Angle     :  0.880  32.510   9243  Z= 0.366
  Chirality :  0.043   0.142   1056
  Planarity :  0.004   0.057   1153
  Dihedral  :  7.346  89.867   1055
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 21.47 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.30), residues: 853
  helix:  2.53 (0.44), residues: 141
  sheet:  0.62 (0.28), residues: 351
  loop :  0.47 (0.36), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K  72 
 TYR   0.011   0.001   TYR K 104 
 PHE   0.012   0.001   PHE B 261 
 TRP   0.010   0.001   TRP H 125 
 HIS   0.001   0.000   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6785)
  covalent geometry    : angle       0.87999 ( 9231)
  SS BOND              : bond        0.00226 (    6)
  SS BOND              : angle       1.09279 (   12)
  hydrogen bonds       : bond        0.03818 (  314)
  hydrogen bonds       : angle       5.11932 (  891)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8726 (mm)
REVERT: A  157 LYS cc_start: 0.8580 (tptm) cc_final: 0.8352 (tptp)
REVERT: A  159 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8295 (mm-30)
REVERT: B  250 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8652 (tttp)
REVERT: L   49 ARG cc_start: 0.8876 (ttp-170) cc_final: 0.8403 (ttp-110)
REVERT: L   95 ASP cc_start: 0.8863 (m-30) cc_final: 0.8121 (m-30)
REVERT: L  130 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8207 (mt-10)
REVERT: L  180 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8022 (pt0)
REVERT: H  178 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8818 (mp)
REVERT: H  239 ASN cc_start: 0.9167 (t0) cc_final: 0.8870 (t0)
REVERT: H  246 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8842 (mmmt)
REVERT: K    4 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7845 (pp)
REVERT: K   44 GLU cc_start: 0.8708 (pm20) cc_final: 0.8490 (pm20)
  outliers start: 27
  outliers final: 8
  residues processed: 121
  average time/residue: 0.5574
  time to fit residues: 70.3442
Evaluate side-chains
  117 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  130 GLU
Chi-restraints excluded: chain L residue  180 GLN
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  246 LYS
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   74 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0670
   chunk 2 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.089496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.065516 restraints weight = 22902.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.2691 rms_B_bonded: 3.01
r_work: 0.2551 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2551
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2557
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2557 r_free = 0.2557    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2557 r_free = 0.2557    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2557
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8821
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6791  Z= 0.156
  Angle     :  0.873  31.912   9243  Z= 0.360
  Chirality :  0.042   0.151   1056
  Planarity :  0.004   0.050   1153
  Dihedral  :  7.201  90.971   1052
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 22.16 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.31), residues: 853
  helix:  2.34 (0.44), residues: 144
  sheet:  0.73 (0.29), residues: 338
  loop :  0.34 (0.35), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  53 
 TYR   0.019   0.001   TYR A  67 
 PHE   0.011   0.001   PHE B 261 
 TRP   0.010   0.001   TRP A  18 
 HIS   0.001   0.000   HIS H 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 6785)
  covalent geometry    : angle       0.87236 ( 9231)
  SS BOND              : bond        0.00203 (    6)
  SS BOND              : angle       1.01820 (   12)
  hydrogen bonds       : bond        0.03578 (  314)
  hydrogen bonds       : angle       4.94524 (  891)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  130 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8742 (mm)
REVERT: L   49 ARG cc_start: 0.8911 (ttp-170) cc_final: 0.8439 (ttp-110)
REVERT: L   95 ASP cc_start: 0.8849 (m-30) cc_final: 0.8048 (m-30)
REVERT: L  130 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8196 (mt-10)
REVERT: H  239 ASN cc_start: 0.9166 (t0) cc_final: 0.8867 (t0)
REVERT: H  246 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8840 (mmmt)
REVERT: K    4 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7705 (pp)
REVERT: K   34 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8797 (mmm)
  outliers start: 27
  outliers final: 10
  residues processed: 120
  average time/residue: 0.6265
  time to fit residues: 78.5979
Evaluate side-chains
  114 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  130 GLU
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain H residue  246 LYS
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   11 LEU
Chi-restraints excluded: chain K residue   34 MET
Chi-restraints excluded: chain K residue   74 ASP
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue  109 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 20 optimal weight:    0.3980
   chunk 10 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.089455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.066432 restraints weight = 17398.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 2.63
r_work: 0.2578 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2436 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2436
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2445
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2445 r_free = 0.2445    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2445 r_free = 0.2445    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2445
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8900
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6791  Z= 0.161
  Angle     :  0.875  31.831   9243  Z= 0.362
  Chirality :  0.042   0.145   1056
  Planarity :  0.004   0.046   1153
  Dihedral  :  7.218  91.935   1052
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 22.71 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.30), residues: 853
  helix:  2.33 (0.44), residues: 144
  sheet:  0.81 (0.29), residues: 335
  loop :  0.37 (0.35), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  53 
 TYR   0.010   0.001   TYR A  67 
 PHE   0.011   0.001   PHE B 261 
 TRP   0.010   0.001   TRP A  18 
 HIS   0.001   0.000   HIS H  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6785)
  covalent geometry    : angle       0.87534 ( 9231)
  SS BOND              : bond        0.00226 (    6)
  SS BOND              : angle       0.99389 (   12)
  hydrogen bonds       : bond        0.03511 (  314)
  hydrogen bonds       : angle       4.88270 (  891)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8807 (mm)
REVERT: L   49 ARG cc_start: 0.9013 (ttp-170) cc_final: 0.8555 (ttp-110)
REVERT: L   95 ASP cc_start: 0.8933 (m-30) cc_final: 0.8216 (m-30)
REVERT: L  190 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8549 (mm-30)
REVERT: H  178 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8792 (mp)
REVERT: K    4 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7818 (pp)
REVERT: K   34 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8977 (mmm)
  outliers start: 24
  outliers final: 12
  residues processed: 116
  average time/residue: 0.5845
  time to fit residues: 71.0702
Evaluate side-chains
  114 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   11 LEU
Chi-restraints excluded: chain K residue   34 MET
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue  109 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 34 optimal weight:    0.2980
   chunk 72 optimal weight:    0.0170
   chunk 49 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 68 optimal weight:    0.4980
   chunk 32 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.090519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.066765 restraints weight = 22497.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.2713 rms_B_bonded: 2.94
r_work: 0.2576 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2584
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2584 r_free = 0.2584    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2583 r_free = 0.2583    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2583
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8830
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6791  Z= 0.127
  Angle     :  0.861  31.584   9243  Z= 0.353
  Chirality :  0.041   0.146   1056
  Planarity :  0.004   0.044   1153
  Dihedral  :  7.143  91.680   1052
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 23.27 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.31), residues: 853
  helix:  2.44 (0.45), residues: 144
  sheet:  0.88 (0.29), residues: 336
  loop :  0.39 (0.35), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  53 
 TYR   0.009   0.001   TYR K 110 
 PHE   0.009   0.001   PHE B 316 
 TRP   0.011   0.001   TRP A  18 
 HIS   0.001   0.000   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6785)
  covalent geometry    : angle       0.86124 ( 9231)
  SS BOND              : bond        0.00153 (    6)
  SS BOND              : angle       0.85264 (   12)
  hydrogen bonds       : bond        0.03250 (  314)
  hydrogen bonds       : angle       4.74819 (  891)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLN cc_start: 0.7238 (tm-30) cc_final: 0.6835 (tm-30)
REVERT: A  130 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8740 (mm)
REVERT: L   49 ARG cc_start: 0.8862 (ttp-170) cc_final: 0.8457 (ttp-110)
REVERT: L   95 ASP cc_start: 0.8857 (m-30) cc_final: 0.7997 (m-30)
REVERT: H  178 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8718 (mp)
REVERT: H  239 ASN cc_start: 0.9120 (t0) cc_final: 0.8724 (t0)
REVERT: K    4 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7791 (pp)
  outliers start: 21
  outliers final: 8
  residues processed: 119
  average time/residue: 0.5318
  time to fit residues: 66.4533
Evaluate side-chains
  114 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue  109 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0980
   chunk 23 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0020
   overall best weight:    0.4988

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.090977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.066764 restraints weight = 22550.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.2710 rms_B_bonded: 3.07
r_work: 0.2568 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2570 r_free = 0.2570    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2570 r_free = 0.2570    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2570
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8810
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6791  Z= 0.135
  Angle     :  0.869  31.558   9243  Z= 0.357
  Chirality :  0.041   0.145   1056
  Planarity :  0.004   0.043   1153
  Dihedral  :  7.129  91.389   1052
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 23.13 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.31), residues: 853
  helix:  2.47 (0.45), residues: 144
  sheet:  0.91 (0.29), residues: 336
  loop :  0.37 (0.35), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 236 
 TYR   0.008   0.001   TYR K 110 
 PHE   0.010   0.001   PHE B 261 
 TRP   0.011   0.001   TRP A  18 
 HIS   0.001   0.000   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6785)
  covalent geometry    : angle       0.86912 ( 9231)
  SS BOND              : bond        0.00186 (    6)
  SS BOND              : angle       0.86097 (   12)
  hydrogen bonds       : bond        0.03253 (  314)
  hydrogen bonds       : angle       4.71195 (  891)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLN cc_start: 0.7283 (tm-30) cc_final: 0.6874 (tm-30)
REVERT: A  130 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8718 (mm)
REVERT: L   49 ARG cc_start: 0.8906 (ttp-170) cc_final: 0.8481 (ttp-110)
REVERT: L   95 ASP cc_start: 0.8884 (m-30) cc_final: 0.8093 (m-30)
REVERT: H  178 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8713 (mp)
REVERT: H  239 ASN cc_start: 0.9084 (t0) cc_final: 0.8657 (t0)
REVERT: K    4 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7756 (pp)
  outliers start: 21
  outliers final: 8
  residues processed: 117
  average time/residue: 0.5318
  time to fit residues: 65.3324
Evaluate side-chains
  112 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue    4 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0270
   chunk 26 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.7642

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.089055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.066894 restraints weight = 14526.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.2723 rms_B_bonded: 2.37
r_work: 0.2595 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2455 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2455
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2456
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2456 r_free = 0.2456    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2456 r_free = 0.2456    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2456
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8919
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6791  Z= 0.174
  Angle     :  0.888  31.606   9243  Z= 0.369
  Chirality :  0.042   0.146   1056
  Planarity :  0.004   0.042   1153
  Dihedral  :  7.197  91.668   1052
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 23.68 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.31), residues: 853
  helix:  2.62 (0.45), residues: 141
  sheet:  0.85 (0.29), residues: 337
  loop :  0.44 (0.36), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  53 
 TYR   0.010   0.001   TYR K 104 
 PHE   0.013   0.001   PHE B 261 
 TRP   0.010   0.001   TRP H 125 
 HIS   0.001   0.000   HIS H  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6785)
  covalent geometry    : angle       0.88814 ( 9231)
  SS BOND              : bond        0.00275 (    6)
  SS BOND              : angle       1.03754 (   12)
  hydrogen bonds       : bond        0.03516 (  314)
  hydrogen bonds       : angle       4.79213 (  891)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7366 (tm-30) cc_final: 0.6903 (tm-30)
REVERT: A  130 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8794 (mm)
REVERT: L   49 ARG cc_start: 0.8970 (ttp-170) cc_final: 0.8764 (ttp-170)
REVERT: H  178 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8720 (mp)
REVERT: K    4 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7885 (pp)
  outliers start: 15
  outliers final: 8
  residues processed: 108
  average time/residue: 0.6363
  time to fit residues: 72.0449
Evaluate side-chains
  108 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   83 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0970
   chunk 47 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
K  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.089880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.067604 restraints weight = 15311.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.2738 rms_B_bonded: 2.44
r_work: 0.2609 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2471 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2477
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2477 r_free = 0.2477    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2477 r_free = 0.2477    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8907
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6791  Z= 0.141
  Angle     :  0.880  31.469   9243  Z= 0.364
  Chirality :  0.041   0.146   1056
  Planarity :  0.004   0.043   1153
  Dihedral  :  7.158  91.248   1052
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 23.27 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.31), residues: 853
  helix:  2.66 (0.45), residues: 141
  sheet:  0.90 (0.29), residues: 336
  loop :  0.46 (0.36), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  53 
 TYR   0.007   0.001   TYR L  61 
 PHE   0.010   0.001   PHE B 261 
 TRP   0.013   0.001   TRP A  18 
 HIS   0.001   0.000   HIS H 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6785)
  covalent geometry    : angle       0.87997 ( 9231)
  SS BOND              : bond        0.00184 (    6)
  SS BOND              : angle       0.87591 (   12)
  hydrogen bonds       : bond        0.03299 (  314)
  hydrogen bonds       : angle       4.72502 (  891)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7335 (tm-30) cc_final: 0.6843 (tm-30)
REVERT: A  130 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8740 (mm)
REVERT: L   49 ARG cc_start: 0.8987 (ttp-170) cc_final: 0.8772 (ttp-170)
REVERT: H  178 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8712 (mp)
REVERT: H  246 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8805 (tmtt)
REVERT: K    4 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7874 (pp)
  outliers start: 18
  outliers final: 8
  residues processed: 110
  average time/residue: 0.6212
  time to fit residues: 71.4280
Evaluate side-chains
  109 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  246 LYS
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue    4 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0170
   chunk 28 optimal weight:    0.4980
   chunk 59 optimal weight:    0.5980
   chunk 73 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0070
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.3036

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
K  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.091999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.068726 restraints weight = 20573.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 2.82
r_work: 0.2621 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2628 r_free = 0.2628    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2628 r_free = 0.2628    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8798
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6791  Z= 0.112
  Angle     :  0.875  31.325   9243  Z= 0.361
  Chirality :  0.041   0.145   1056
  Planarity :  0.003   0.044   1153
  Dihedral  :  7.047  90.340   1052
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 24.24 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.31), residues: 853
  helix:  2.71 (0.45), residues: 141
  sheet:  1.08 (0.30), residues: 317
  loop :  0.40 (0.34), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  53 
 TYR   0.009   0.001   TYR L  61 
 PHE   0.009   0.001   PHE B 316 
 TRP   0.018   0.001   TRP A  18 
 HIS   0.001   0.000   HIS B 285 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6785)
  covalent geometry    : angle       0.87556 ( 9231)
  SS BOND              : bond        0.00096 (    6)
  SS BOND              : angle       0.69773 (   12)
  hydrogen bonds       : bond        0.03002 (  314)
  hydrogen bonds       : angle       4.56520 (  891)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  130 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8671 (mm)
REVERT: H  178 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8626 (mp)
REVERT: K    4 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7847 (pp)
REVERT: K   62 ASP cc_start: 0.8611 (m-30) cc_final: 0.8364 (t0)
  outliers start: 11
  outliers final: 6
  residues processed: 117
  average time/residue: 0.6388
  time to fit residues: 78.2895
Evaluate side-chains
  110 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue    4 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 51 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 67 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   chunk 21 optimal weight:    0.3980
   chunk 63 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 103 ASN
H 239 ASN
K  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.090554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.068720 restraints weight = 14066.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 2.31
r_work: 0.2631 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2494 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2494
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2500
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2500 r_free = 0.2500    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2500 r_free = 0.2500    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2500
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8875
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6791  Z= 0.146
  Angle     :  0.887  31.374   9243  Z= 0.368
  Chirality :  0.042   0.145   1056
  Planarity :  0.004   0.042   1153
  Dihedral  :  7.077  90.144   1052
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 24.24 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.31), residues: 853
  helix:  2.63 (0.44), residues: 141
  sheet:  0.99 (0.29), residues: 337
  loop :  0.47 (0.36), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  49 
 TYR   0.012   0.001   TYR B 264 
 PHE   0.011   0.001   PHE B 261 
 TRP   0.016   0.001   TRP A  18 
 HIS   0.001   0.000   HIS H  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6785)
  covalent geometry    : angle       0.88681 ( 9231)
  SS BOND              : bond        0.00209 (    6)
  SS BOND              : angle       0.94272 (   12)
  hydrogen bonds       : bond        0.03265 (  314)
  hydrogen bonds       : angle       4.62167 (  891)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2533.12 seconds
wall clock time: 43 minutes 53.61 seconds (2633.61 seconds total)