Starting phenix.real_space_refine
on Thu Mar 13 04:20:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i9l_35275/03_2025/8i9l_35275.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i9l_35275/03_2025/8i9l_35275.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i9l_35275/03_2025/8i9l_35275.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i9l_35275/03_2025/8i9l_35275.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i9l_35275/03_2025/8i9l_35275.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i9l_35275/03_2025/8i9l_35275.cif"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.026
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      60      5.16       5
     C    5488      2.51       5
     N    1485      2.21       5
     O    1584      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8617
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2421
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 54}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 171
          Unresolved non-hydrogen angles: 214
          Unresolved non-hydrogen dihedrals: 129
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 90
    Chain: "A"
      Number of atoms: 1575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1575
          Classifications: {'peptide': 210}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 4, 'TRANS': 205}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 51
    Chain: "G"
      Number of atoms: 398
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 398
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "H"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1698
          Classifications: {'peptide': 234}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 120
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 47
    Chain: "C"
      Number of atoms: 2056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2056
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 14, 'TRANS': 262}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 135
          Unresolved non-hydrogen angles: 168
          Unresolved non-hydrogen dihedrals: 111
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 69
    Chain: "D"
      Number of atoms: 469
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 469
          Classifications: {'peptide': 70}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 1, 'TRANS': 68}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 101
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 57
  Time building chain proxies: 5.58, per 1000 atoms: 0.65
  Number of scatterers: 8617
  At special positions: 0
  Unit cell: (89.3004, 119.067, 140.329, 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      60     16.00
     O    1584      8.00
     N    1485      7.00
     C    5488      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  95 " - pdb=" SG  CYS C 172 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  49 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  56 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  36 " - pdb=" SG  CYS D  57 " distance=2.03

  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: 2.27
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2202

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      38.4% alpha, 21.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.597A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 33
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 3.917A  pdb=" N   LYS A  32 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.554A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
      removed outlier: 3.769A  pdb=" N   LYS A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLU A 217 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 256
    Processing helix  chain 'A' and resid 271 through 282
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.991A  pdb=" N   VAL A 334 " --> pdb=" O   ASN A 330 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 53 through 56
      removed outlier: 4.028A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 53 through 56'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.772A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 3.602A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 50
      Proline residue:  C  39  - end of helix
    Processing helix  chain 'C' and resid 55 through 84
      removed outlier: 3.878A  pdb=" N   TRP C  60 " --> pdb=" O   VAL C  56 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   PHE C  61 " --> pdb=" O   ASN C  57 " (cutoff:3.500A)
      Proline residue:  C  76  - end of helix
    Processing helix  chain 'C' and resid 91 through 126
      removed outlier: 3.528A  pdb=" N   CYS C  95 " --> pdb=" O   GLY C  91 " (cutoff:3.500A)
      Proline residue:  C  99  - end of helix
      removed outlier: 5.101A  pdb=" N   VAL C 103 " --> pdb=" O   PRO C  99 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 133
      removed outlier: 3.726A  pdb=" N   ASN C 132 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 159
      Proline residue:  C 156  - end of helix
    Processing helix  chain 'C' and resid 332 through 363
      removed outlier: 4.792A  pdb=" N   LEU C 347 " --> pdb=" O   VAL C 343 " (cutoff:3.500A)
      Proline residue:  C 348  - end of helix
    Processing helix  chain 'C' and resid 374 through 390
    Processing helix  chain 'C' and resid 390 through 403
      removed outlier: 3.999A  pdb=" N   LEU C 401 " --> pdb=" O   GLY C 397 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU C 402 " --> pdb=" O   VAL C 398 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 407 through 436
      removed outlier: 3.834A  pdb=" N   HIS C 418 " --> pdb=" O   MET C 414 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   VAL C 419 " --> pdb=" O   SER C 415 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   SER C 428 " --> pdb=" O   ALA C 424 " (cutoff:3.500A)
      Proline residue:  C 432  - end of helix
    Processing helix  chain 'C' and resid 439 through 450
    Processing helix  chain 'D' and resid 3 through 13
      removed outlier: 3.824A  pdb=" N   LYS D   7 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
      removed outlier: 4.214A  pdb=" N   ALA D  48 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 45 through 48'
    Processing helix  chain 'D' and resid 49 through 71
      removed outlier: 3.684A  pdb=" N   ASN D  58 " --> pdb=" O   LEU D  54 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.579A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.012A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.102A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.056A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.619A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.694A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.623A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.997A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 275
      removed outlier: 3.991A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 186 through 192
      removed outlier: 3.866A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.898A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.368A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141
      removed outlier: 3.593A  pdb=" N   ALA H 211 " --> pdb=" O   SER H 208 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 149
      removed outlier: 3.963A  pdb=" N   GLU H 246 " --> pdb=" O   VAL H 147 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL H 149 " --> pdb=" O   GLU H 246 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 162 through 163

    465 hydrogen bonds defined for protein.
    1311 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.45

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2803
        1.34 -     1.46: 1766
        1.46 -     1.58: 4157
        1.58 -     1.70: 0
        1.70 -     1.81: 77
  Bond restraints: 8803
  Sorted by residual:
  bond pdb=" N   THR C 337 "
       pdb=" CA  THR C 337 "
    ideal  model  delta    sigma   weight residual
    1.458  1.497 -0.039 1.30e-02 5.92e+03 8.88e+00
  bond pdb=" N   ASN A  43 "
       pdb=" CA  ASN A  43 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.033 1.29e-02 6.01e+03 6.72e+00
  bond pdb=" N   VAL C 103 "
       pdb=" CA  VAL C 103 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.33e-02 5.65e+03 6.25e+00
  bond pdb=" N   ASP C 167 "
       pdb=" CA  ASP C 167 "
    ideal  model  delta    sigma   weight residual
    1.454  1.483 -0.029 1.17e-02 7.31e+03 6.19e+00
  bond pdb=" N   LEU D  75 "
       pdb=" CA  LEU D  75 "
    ideal  model  delta    sigma   weight residual
    1.462  1.497 -0.035 1.48e-02 4.57e+03 5.64e+00
  ... (remaining 8798 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 11816
        2.06 -     4.12: 145
        4.12 -     6.17: 31
        6.17 -     8.23: 5
        8.23 -    10.29: 1
  Bond angle restraints: 11998
  Sorted by residual:
  angle pdb=" N   LEU D  73 "
        pdb=" CA  LEU D  73 "
        pdb=" C   LEU D  73 "
      ideal   model   delta    sigma   weight residual
     108.67   98.38   10.29 1.55e+00 4.16e-01 4.41e+01
  angle pdb=" N   ILE C 163 "
        pdb=" CA  ILE C 163 "
        pdb=" C   ILE C 163 "
      ideal   model   delta    sigma   weight residual
     107.75   99.79    7.96 1.46e+00 4.69e-01 2.97e+01
  angle pdb=" C   PHE D  42 "
        pdb=" CA  PHE D  42 "
        pdb=" CB  PHE D  42 "
      ideal   model   delta    sigma   weight residual
     115.79  109.69    6.10 1.19e+00 7.06e-01 2.63e+01
  angle pdb=" N   LEU D  75 "
        pdb=" CA  LEU D  75 "
        pdb=" C   LEU D  75 "
      ideal   model   delta    sigma   weight residual
     112.47  117.52   -5.05 1.24e+00 6.50e-01 1.66e+01
  angle pdb=" N   LEU A  13 "
        pdb=" CA  LEU A  13 "
        pdb=" C   LEU A  13 "
      ideal   model   delta    sigma   weight residual
     111.28  107.18    4.10 1.09e+00 8.42e-01 1.42e+01
  ... (remaining 11993 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.29: 4624
       16.29 -    32.59: 425
       32.59 -    48.88: 77
       48.88 -    65.18: 8
       65.18 -    81.47: 7
  Dihedral angle restraints: 5141
    sinusoidal: 1731
      harmonic: 3410
  Sorted by residual:
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  49 "
           pdb=" CB  CYS D  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -52.60  -33.40     1      1.00e+01 1.00e-02 1.59e+01
  dihedral pdb=" CB  CYS D  23 "
           pdb=" SG  CYS D  23 "
           pdb=" SG  CYS D  56 "
           pdb=" CB  CYS D  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -115.09   29.09     1      1.00e+01 1.00e-02 1.21e+01
  dihedral pdb=" CA  PRO C  99 "
           pdb=" C   PRO C  99 "
           pdb=" N   SER C 100 "
           pdb=" CA  SER C 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.12   16.88     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 5138 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1189
       0.056 -    0.112: 186
       0.112 -    0.168: 19
       0.168 -    0.223: 2
       0.223 -    0.279: 2
  Chirality restraints: 1398
  Sorted by residual:
  chirality pdb=" CA  LEU D  73 "
            pdb=" N   LEU D  73 "
            pdb=" C   LEU D  73 "
            pdb=" CB  LEU D  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CA  ILE C 163 "
            pdb=" N   ILE C 163 "
            pdb=" C   ILE C 163 "
            pdb=" CB  ILE C 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  VAL A 202 "
            pdb=" CA  VAL A 202 "
            pdb=" CG1 VAL A 202 "
            pdb=" CG2 VAL A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1395 not shown)

  Planarity restraints: 1535
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 162 "   -0.023 2.00e-02 2.50e+03   4.86e-02 2.36e+01
        pdb=" C   GLU C 162 "    0.084 2.00e-02 2.50e+03
        pdb=" O   GLU C 162 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   ILE C 163 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS D  72 "    0.023 2.00e-02 2.50e+03   4.64e-02 2.16e+01
        pdb=" C   HIS D  72 "   -0.080 2.00e-02 2.50e+03
        pdb=" O   HIS D  72 "    0.030 2.00e-02 2.50e+03
        pdb=" N   LEU D  73 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY D  74 "   -0.019 2.00e-02 2.50e+03   3.78e-02 1.43e+01
        pdb=" C   GLY D  74 "    0.065 2.00e-02 2.50e+03
        pdb=" O   GLY D  74 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LEU D  75 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1532 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1503
        2.77 -     3.30: 8306
        3.30 -     3.83: 14508
        3.83 -     4.37: 16466
        4.37 -     4.90: 29548
  Nonbonded interactions: 70331
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 165 "
            pdb=" O   PHE B 180 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASP B 154 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   PHE H  32 "
            pdb=" NH2 ARG H  72 "
     model   vdw
     2.306 3.120
  ... (remaining 70326 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=1.00 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:             2.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.210
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8803  Z= 0.167
  Angle     :  0.582  10.291  11998  Z= 0.345
  Chirality :  0.042   0.279   1398
  Planarity :  0.004   0.057   1535
  Dihedral  : 12.918  81.470   2921
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  0.84 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.26), residues: 1161
  helix:  1.79 (0.27), residues: 419
  sheet: -0.40 (0.31), residues: 276
  loop : -0.82 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 111 
 HIS   0.003   0.001   HIS C 418 
 PHE   0.016   0.001   PHE C 430 
 TYR   0.016   0.001   TYR A 231 
 ARG   0.008   0.000   ARG H 160 

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6632 (mtm110)
REVERT: D   72 HIS cc_start: 0.7071 (m90) cc_final: 0.6757 (m90)
REVERT: D   73 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7408 (tm)
  outliers start: 8
  outliers final: 3
  residues processed: 151
  average time/residue: 0.2474
  time to fit residues: 49.2919
Evaluate side-chains
  134 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 129
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue  231 TYR
Chi-restraints excluded: chain C residue  393 TYR
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   77 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.1980
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:    9.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
H 113 GLN
C  41 ASN
D  66 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.138292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.112443 restraints weight = 13895.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 1.98
r_work: 0.3472 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8803  Z= 0.305
  Angle     :  0.590   6.679  11998  Z= 0.312
  Chirality :  0.045   0.193   1398
  Planarity :  0.004   0.046   1535
  Dihedral  :  5.158  70.705   1270
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  :  8.25 %
    Favored  : 89.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.26), residues: 1161
  helix:  1.68 (0.27), residues: 427
  sheet: -0.44 (0.31), residues: 280
  loop : -0.74 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  60 
 HIS   0.007   0.001   HIS B 142 
 PHE   0.025   0.002   PHE C 151 
 TYR   0.014   0.002   TYR D  59 
 ARG   0.005   0.001   ARG B  46 

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
REVERT: B  258 ASP cc_start: 0.7168 (t0) cc_final: 0.6713 (t0)
REVERT: A   10 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6839 (mtt180)
REVERT: H  178 LEU cc_start: 0.8085 (tp) cc_final: 0.7819 (tp)
REVERT: C   88 TRP cc_start: 0.7187 (t-100) cc_final: 0.6940 (t-100)
REVERT: C  340 ARG cc_start: 0.7602 (ttm170) cc_final: 0.6674 (ttm110)
REVERT: D   72 HIS cc_start: 0.7575 (m90) cc_final: 0.7359 (m-70)
REVERT: D   73 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7542 (tm)
  outliers start: 15
  outliers final: 9
  residues processed: 142
  average time/residue: 0.2302
  time to fit residues: 43.8573
Evaluate side-chains
  143 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  220 THR
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain C residue  393 TYR
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   chunk 109 optimal weight:    4.9990
   chunk 112 optimal weight:    0.0030
   chunk 10 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 57 optimal weight:    0.1980
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.139239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.113285 restraints weight = 14096.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.05
r_work: 0.3474 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8803  Z= 0.199
  Angle     :  0.535   6.769  11998  Z= 0.281
  Chirality :  0.042   0.164   1398
  Planarity :  0.004   0.039   1535
  Dihedral  :  4.859  72.790   1264
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 11.72 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.26), residues: 1161
  helix:  1.74 (0.26), residues: 422
  sheet: -0.37 (0.31), residues: 269
  loop : -0.81 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 297 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.022   0.001   PHE C 151 
 TYR   0.014   0.001   TYR D  59 
 ARG   0.006   0.000   ARG B  46 

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: B  298 ASP cc_start: 0.7934 (t70) cc_final: 0.7626 (t70)
REVERT: H  178 LEU cc_start: 0.8030 (tp) cc_final: 0.7772 (tp)
REVERT: C   88 TRP cc_start: 0.7203 (t-100) cc_final: 0.6964 (t-100)
REVERT: C  340 ARG cc_start: 0.7448 (ttm170) cc_final: 0.6489 (ttm110)
REVERT: D   73 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8014 (tm)
  outliers start: 8
  outliers final: 5
  residues processed: 141
  average time/residue: 0.2277
  time to fit residues: 43.6357
Evaluate side-chains
  136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  393 TYR
Chi-restraints excluded: chain C residue  407 THR
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 115 optimal weight:    0.0170
   chunk 12 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 102 optimal weight:    0.7980
   chunk 113 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.141865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.114389 restraints weight = 13921.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.16
r_work: 0.3439 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3297 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8803  Z= 0.283
  Angle     :  0.572   8.164  11998  Z= 0.298
  Chirality :  0.043   0.187   1398
  Planarity :  0.004   0.036   1535
  Dihedral  :  4.784  75.272   1260
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.28 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.26), residues: 1161
  helix:  1.68 (0.26), residues: 422
  sheet: -0.43 (0.31), residues: 274
  loop : -0.88 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.018   0.002   PHE C 430 
 TYR   0.014   0.002   TYR C 435 
 ARG   0.006   0.000   ARG H 160 

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7529 (mp)
REVERT: A  244 MET cc_start: 0.4806 (tpt) cc_final: 0.4605 (tpp)
REVERT: A  299 ASP cc_start: 0.7344 (t0) cc_final: 0.7075 (t0)
REVERT: C   88 TRP cc_start: 0.7269 (t-100) cc_final: 0.7036 (t-100)
REVERT: C  337 THR cc_start: 0.5578 (t) cc_final: 0.5369 (t)
REVERT: C  340 ARG cc_start: 0.7483 (ttm170) cc_final: 0.6510 (ttm110)
  outliers start: 15
  outliers final: 10
  residues processed: 144
  average time/residue: 0.2361
  time to fit residues: 45.9707
Evaluate side-chains
  140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  343 VAL
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 77 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0370
   chunk 69 optimal weight:    0.2980
   chunk 109 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0980
   chunk 62 optimal weight:    0.4980
   overall best weight:    0.3258

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

Flipped N/Q/H residues before XYZ refinement:
C 427 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.143484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.116250 restraints weight = 13852.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 2.16
r_work: 0.3455 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8803  Z= 0.180
  Angle     :  0.529   7.501  11998  Z= 0.276
  Chirality :  0.042   0.164   1398
  Planarity :  0.004   0.038   1535
  Dihedral  :  4.650  74.797   1258
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.95 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 1161
  helix:  1.73 (0.26), residues: 421
  sheet: -0.45 (0.31), residues: 269
  loop : -0.85 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS D  72 
 PHE   0.015   0.001   PHE C 151 
 TYR   0.013   0.001   TYR C 435 
 ARG   0.006   0.000   ARG H 160 

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7629 (mp)
REVERT: B  298 ASP cc_start: 0.7927 (t70) cc_final: 0.7615 (t70)
REVERT: B  301 LYS cc_start: 0.8209 (mmpt) cc_final: 0.7924 (mmmt)
REVERT: A   10 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6783 (mtt180)
REVERT: A  299 ASP cc_start: 0.7260 (t0) cc_final: 0.6962 (t0)
REVERT: H  178 LEU cc_start: 0.8107 (tp) cc_final: 0.7816 (tp)
REVERT: C   88 TRP cc_start: 0.7219 (t-100) cc_final: 0.6974 (t-100)
REVERT: C  337 THR cc_start: 0.5476 (t) cc_final: 0.5261 (t)
REVERT: C  340 ARG cc_start: 0.7413 (ttm170) cc_final: 0.6453 (ttm110)
REVERT: C  443 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7319 (ttm170)
  outliers start: 15
  outliers final: 6
  residues processed: 145
  average time/residue: 0.2169
  time to fit residues: 42.5015
Evaluate side-chains
  142 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  443 ARG
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0070
   chunk 14 optimal weight:    0.4980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.5798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.142013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.114630 restraints weight = 13837.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.15
r_work: 0.3444 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8803  Z= 0.255
  Angle     :  0.557   7.633  11998  Z= 0.291
  Chirality :  0.043   0.181   1398
  Planarity :  0.004   0.037   1535
  Dihedral  :  4.726  75.178   1258
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.15 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.25), residues: 1161
  helix:  1.71 (0.26), residues: 421
  sheet: -0.56 (0.31), residues: 273
  loop : -0.88 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.027   0.001   PHE C 151 
 TYR   0.013   0.002   TYR C 435 
 ARG   0.007   0.000   ARG H 160 

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7527 (mp)
REVERT: A   10 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6809 (mtt180)
REVERT: A  299 ASP cc_start: 0.7299 (t0) cc_final: 0.6997 (t0)
REVERT: H   77 ASN cc_start: 0.8046 (t0) cc_final: 0.7596 (t0)
REVERT: C   88 TRP cc_start: 0.7310 (t-100) cc_final: 0.7079 (t-100)
REVERT: C  337 THR cc_start: 0.5648 (t) cc_final: 0.5428 (t)
REVERT: C  340 ARG cc_start: 0.7463 (ttm170) cc_final: 0.6513 (ttm110)
REVERT: C  437 LEU cc_start: 0.7007 (mp) cc_final: 0.6377 (mp)
REVERT: C  443 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7428 (ttm170)
  outliers start: 18
  outliers final: 11
  residues processed: 151
  average time/residue: 0.2447
  time to fit residues: 49.4112
Evaluate side-chains
  149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  443 ARG
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 77 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0870
   chunk 22 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0870
   chunk 1 optimal weight:    0.7980
   chunk 82 optimal weight:    0.2980
   chunk 73 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0270
   overall best weight:    0.2394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.139789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.114196 restraints weight = 14071.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 2.01
r_work: 0.3503 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8803  Z= 0.157
  Angle     :  0.520   8.720  11998  Z= 0.272
  Chirality :  0.042   0.147   1398
  Planarity :  0.003   0.038   1535
  Dihedral  :  4.563  73.312   1258
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.75 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 1161
  helix:  1.74 (0.26), residues: 421
  sheet: -0.58 (0.31), residues: 267
  loop : -0.77 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.022   0.001   PHE C 151 
 TYR   0.013   0.001   TYR C 435 
 ARG   0.007   0.000   ARG H 160 

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7583 (mp)
REVERT: B  298 ASP cc_start: 0.7894 (t70) cc_final: 0.7551 (t0)
REVERT: A   10 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6647 (mtt180)
REVERT: A  299 ASP cc_start: 0.7201 (t0) cc_final: 0.6918 (t0)
REVERT: H   83 MET cc_start: 0.7581 (ptt) cc_final: 0.7288 (ptt)
REVERT: H  178 LEU cc_start: 0.8112 (tp) cc_final: 0.7816 (tp)
REVERT: C   88 TRP cc_start: 0.7199 (t-100) cc_final: 0.6952 (t-100)
REVERT: C  337 THR cc_start: 0.5482 (t) cc_final: 0.5259 (t)
REVERT: C  340 ARG cc_start: 0.7392 (ttm170) cc_final: 0.6535 (ttm110)
REVERT: C  443 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7621 (mtm180)
  outliers start: 15
  outliers final: 9
  residues processed: 145
  average time/residue: 0.2361
  time to fit residues: 46.4471
Evaluate side-chains
  143 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  301 LYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  443 ARG
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 107 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 33 optimal weight:    0.4980
   chunk 114 optimal weight:    0.8980
   chunk 74 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 95 optimal weight:    0.2980
   chunk 65 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.143049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.115589 restraints weight = 14092.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3569 rms_B_bonded: 2.18
r_work: 0.3451 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8803  Z= 0.241
  Angle     :  0.558   9.577  11998  Z= 0.288
  Chirality :  0.043   0.175   1398
  Planarity :  0.004   0.040   1535
  Dihedral  :  4.648  73.044   1258
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.87 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.26), residues: 1161
  helix:  1.73 (0.26), residues: 421
  sheet: -0.58 (0.31), residues: 279
  loop : -0.79 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.021   0.001   PHE C 151 
 TYR   0.015   0.002   TYR C 435 
 ARG   0.008   0.000   ARG H 160 

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7535 (mp)
REVERT: A   10 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6734 (mtt180)
REVERT: A  244 MET cc_start: 0.4939 (tpt) cc_final: 0.4646 (tpp)
REVERT: A  299 ASP cc_start: 0.7269 (t0) cc_final: 0.6975 (t0)
REVERT: H  178 LEU cc_start: 0.8127 (tp) cc_final: 0.7816 (tp)
REVERT: C   88 TRP cc_start: 0.7278 (t-100) cc_final: 0.7039 (t-100)
REVERT: C  337 THR cc_start: 0.5604 (t) cc_final: 0.5376 (t)
REVERT: C  340 ARG cc_start: 0.7448 (ttm170) cc_final: 0.6498 (ttm110)
REVERT: C  443 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7389 (ttm170)
  outliers start: 16
  outliers final: 8
  residues processed: 143
  average time/residue: 0.2281
  time to fit residues: 44.0095
Evaluate side-chains
  141 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  443 ARG
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0470
   chunk 83 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.5878

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.142679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.115232 restraints weight = 13987.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.17
r_work: 0.3446 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8803  Z= 0.256
  Angle     :  0.564   9.875  11998  Z= 0.293
  Chirality :  0.044   0.186   1398
  Planarity :  0.004   0.040   1535
  Dihedral  :  4.711  72.520   1258
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.34 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.26), residues: 1161
  helix:  1.67 (0.26), residues: 420
  sheet: -0.62 (0.31), residues: 279
  loop : -0.82 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  99 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.020   0.002   PHE C 151 
 TYR   0.016   0.002   TYR H  60 
 ARG   0.008   0.000   ARG H 160 

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
REVERT: B  273 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7551 (mp)
REVERT: A   10 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6716 (mtt180)
REVERT: A  244 MET cc_start: 0.4906 (tpt) cc_final: 0.4682 (tpp)
REVERT: A  299 ASP cc_start: 0.7302 (t0) cc_final: 0.7011 (t0)
REVERT: C   88 TRP cc_start: 0.7294 (t-100) cc_final: 0.7057 (t-100)
REVERT: C  337 THR cc_start: 0.5793 (t) cc_final: 0.5529 (t)
REVERT: C  340 ARG cc_start: 0.7438 (ttm170) cc_final: 0.6524 (ttm110)
REVERT: C  443 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7482 (ttm170)
  outliers start: 17
  outliers final: 11
  residues processed: 145
  average time/residue: 0.2208
  time to fit residues: 43.4141
Evaluate side-chains
  145 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  443 ARG
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0970
   chunk 76 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 61 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.142222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.114852 restraints weight = 13901.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 2.16
r_work: 0.3436 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8803  Z= 0.282
  Angle     :  0.585  10.462  11998  Z= 0.302
  Chirality :  0.044   0.168   1398
  Planarity :  0.004   0.040   1535
  Dihedral  :  4.744  71.202   1258
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 17.70 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.26), residues: 1161
  helix:  1.65 (0.27), residues: 420
  sheet: -0.65 (0.31), residues: 279
  loop : -0.84 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  99 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.020   0.002   PHE C 151 
 TYR   0.016   0.002   TYR H  60 
 ARG   0.008   0.000   ARG H 160 

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
REVERT: B   13 GLN cc_start: 0.7842 (pp30) cc_final: 0.7637 (pp30)
REVERT: B  273 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7548 (mp)
REVERT: A   10 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6755 (mtt180)
REVERT: A  299 ASP cc_start: 0.7323 (t0) cc_final: 0.7030 (t0)
REVERT: C   88 TRP cc_start: 0.7313 (t-100) cc_final: 0.7072 (t-100)
REVERT: C  337 THR cc_start: 0.5860 (t) cc_final: 0.5594 (t)
REVERT: C  340 ARG cc_start: 0.7458 (ttm170) cc_final: 0.6568 (ttm110)
REVERT: C  443 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7458 (ttm170)
  outliers start: 14
  outliers final: 10
  residues processed: 143
  average time/residue: 0.2196
  time to fit residues: 42.5964
Evaluate side-chains
  145 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain H residue  213 THR
Chi-restraints excluded: chain C residue  155 ILE
Chi-restraints excluded: chain C residue  334 VAL
Chi-restraints excluded: chain C residue  443 ARG
Chi-restraints excluded: chain D residue   73 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 86 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.141475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.114166 restraints weight = 14105.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.15
r_work: 0.3433 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8803  Z= 0.283
  Angle     :  0.580  10.386  11998  Z= 0.302
  Chirality :  0.044   0.164   1398
  Planarity :  0.004   0.040   1535
  Dihedral  :  4.765  69.806   1258
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 17.82 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.26), residues: 1161
  helix:  1.65 (0.26), residues: 420
  sheet: -0.65 (0.32), residues: 267
  loop : -0.83 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  99 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.028   0.002   PHE C 151 
 TYR   0.016   0.002   TYR H  60 
 ARG   0.009   0.000   ARG H 160 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5610.23 seconds
wall clock time: 96 minutes 29.90 seconds (5789.90 seconds total)