Starting phenix.real_space_refine
on Tue Feb 13 17:30:32 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efq_28088/02_2024/8efq_28088_neut_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efq_28088/02_2024/8efq_28088.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efq_28088/02_2024/8efq_28088.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efq_28088/02_2024/8efq_28088.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efq_28088/02_2024/8efq_28088_neut_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efq_28088/02_2024/8efq_28088_neut_updated.pdb"
  }
  resolution = 3.3
  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=  -0.001 sd=   0.083
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      61      5.16       5
     C    4500      2.51       5
     N    1190      2.21       5
     O    1295      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R ARG  282": "NH1" <-> "NH2"
    Residue "R PHE  345": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 7046
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1747
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2583
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 407
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "P"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 33
          Classifications: {'peptide': 4}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'TRANS': 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'MEA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 2272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2272
          Classifications: {'peptide': 283}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272}
    Chain: "P"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'ETA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.07, per 1000 atoms: 0.58
  Number of scatterers: 7046
  At special positions: 0
  Unit cell: (79.254, 103.887, 139.23, 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      61     16.00
     O    1295      8.00
     N    1190      7.00
     C    4500      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 142 " - pdb=" SG  CYS R 219 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.53
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAL P   2 "
  Number of C-beta restraints generated:  1692

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      22 helices and 9 sheets defined
      43.0% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.928A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 52
    Processing helix  chain 'A' and resid 212 through 215
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 257 through 259
      No H-bonds generated for 'chain 'A' and resid 257 through 259'
    Processing helix  chain 'A' and resid 271 through 279
      removed outlier: 4.068A  pdb=" N   GLU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.891A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 6 through 25
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'G' and resid 10 through 23
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'R' and resid 68 through 97
    Processing helix  chain 'R' and resid 104 through 132
      removed outlier: 3.658A  pdb=" N   TYR R 108 " --> pdb=" O   ALA R 104 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   THR R 122 " --> pdb=" O   LEU R 118 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   LEU R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      Proline residue:  R 124  - end of helix
      removed outlier: 3.734A  pdb=" N   VAL R 128 " --> pdb=" O   PRO R 124 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ASN R 129 " --> pdb=" O   PHE R 125 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   TYR R 130 " --> pdb=" O   GLN R 126 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU R 131 " --> pdb=" O   SER R 127 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 172
      removed outlier: 3.709A  pdb=" N   MET R 153 " --> pdb=" O   ASP R 149 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 180
      removed outlier: 3.687A  pdb=" N   LEU R 178 " --> pdb=" O   PRO R 174 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   ASP R 179 " --> pdb=" O   VAL R 175 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 207
      removed outlier: 4.002A  pdb=" N   ILE R 200 " --> pdb=" O   LEU R 196 " (cutoff:3.500A)
      Proline residue:  R 203  - end of helix
    Processing helix  chain 'R' and resid 227 through 263
      removed outlier: 3.640A  pdb=" N   GLU R 231 " --> pdb=" O   THR R 227 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   MET R 245 " --> pdb=" O   PHE R 241 " (cutoff:3.500A)
      Proline residue:  R 246  - end of helix
      removed outlier: 3.793A  pdb=" N   SER R 263 " --> pdb=" O   LEU R 259 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 271 through 307
      removed outlier: 3.838A  pdb=" N   ASN R 276 " --> pdb=" O   GLU R 272 " (cutoff:3.500A)
      Proline residue:  R 297  - end of helix
    Processing helix  chain 'R' and resid 314 through 338
      removed outlier: 3.765A  pdb=" N   HIS R 321 " --> pdb=" O   THR R 317 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASN R 330 " --> pdb=" O   LEU R 326 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   SER R 331 " --> pdb=" O   GLY R 327 " (cutoff:3.500A)
      Proline residue:  R 335  - end of helix
    Processing helix  chain 'R' and resid 343 through 348
    Processing sheet with id=  A, first strand: chain 'A' and resid 319 through 323
      removed outlier: 6.882A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASN A 269 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ASP A 200 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   VAL A 185 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 92 through 94
      removed outlier: 4.024A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.497A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.979A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 221 through 223
      removed outlier: 4.298A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.924A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.936A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.804A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 46 through 51
      removed outlier: 7.044A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'R' and resid 208 through 212

    345 hydrogen bonds defined for protein.
    1020 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: 1.95

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2236
        1.34 -     1.46: 1370
        1.46 -     1.58: 3492
        1.58 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 7186
  Sorted by residual:
  bond pdb=" C   THR R 296 "
       pdb=" N   PRO R 297 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.023 1.23e-02 6.61e+03 3.43e+00
  bond pdb=" C   MET R 245 "
       pdb=" N   PRO R 246 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.20e-02 6.94e+03 2.45e+00
  bond pdb=" CA  THR B  87 "
       pdb=" C   THR B  87 "
    ideal  model  delta    sigma   weight residual
    1.522  1.544 -0.022 1.51e-02 4.39e+03 2.10e+00
  bond pdb=" C   LEU R 202 "
       pdb=" N   PRO R 203 "
    ideal  model  delta    sigma   weight residual
    1.336  1.353 -0.017 1.23e-02 6.61e+03 1.95e+00
  bond pdb=" CA  MET R 245 "
       pdb=" C   MET R 245 "
    ideal  model  delta    sigma   weight residual
    1.520  1.537 -0.016 1.23e-02 6.61e+03 1.76e+00
  ... (remaining 7181 not shown)

  Histogram of bond angle deviations from ideal:
       99.47 -   106.38: 150
      106.38 -   113.30: 3911
      113.30 -   120.21: 2632
      120.21 -   127.13: 2964
      127.13 -   134.05: 71
  Bond angle restraints: 9728
  Sorted by residual:
  angle pdb=" N   LEU R 123 "
        pdb=" CA  LEU R 123 "
        pdb=" C   LEU R 123 "
      ideal   model   delta    sigma   weight residual
     109.81  117.08   -7.27 2.21e+00 2.05e-01 1.08e+01
  angle pdb=" CA  LEU B  79 "
        pdb=" CB  LEU B  79 "
        pdb=" CG  LEU B  79 "
      ideal   model   delta    sigma   weight residual
     116.30  127.61  -11.31 3.50e+00 8.16e-02 1.04e+01
  angle pdb=" N   THR B 184 "
        pdb=" CA  THR B 184 "
        pdb=" C   THR B 184 "
      ideal   model   delta    sigma   weight residual
     113.02  108.59    4.43 1.49e+00 4.50e-01 8.84e+00
  angle pdb=" N   LYS B  78 "
        pdb=" CA  LYS B  78 "
        pdb=" C   LYS B  78 "
      ideal   model   delta    sigma   weight residual
     108.69  113.91   -5.22 1.77e+00 3.19e-01 8.69e+00
  angle pdb=" C   ASP B 291 "
        pdb=" N   PHE B 292 "
        pdb=" CA  PHE B 292 "
      ideal   model   delta    sigma   weight residual
     124.31  129.21   -4.90 1.67e+00 3.59e-01 8.62e+00
  ... (remaining 9723 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.10: 4096
       15.10 -    30.20: 148
       30.20 -    45.30: 30
       45.30 -    60.39: 1
       60.39 -    75.49: 1
  Dihedral angle restraints: 4276
    sinusoidal: 1668
      harmonic: 2608
  Sorted by residual:
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.76   18.24     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  ARG A 208 "
           pdb=" C   ARG A 208 "
           pdb=" N   LYS A 209 "
           pdb=" CA  LYS A 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.35  -16.65     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.62   16.38     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 4273 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 869
       0.057 -    0.114: 203
       0.114 -    0.171: 43
       0.171 -    0.228: 6
       0.228 -    0.284: 3
  Chirality restraints: 1124
  Sorted by residual:
  chirality pdb=" CB  VAL A 201 "
            pdb=" CA  VAL A 201 "
            pdb=" CG1 VAL A 201 "
            pdb=" CG2 VAL A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CB  ILE A 264 "
            pdb=" CA  ILE A 264 "
            pdb=" CG1 ILE A 264 "
            pdb=" CG2 ILE A 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CB  ILE B  43 "
            pdb=" CA  ILE B  43 "
            pdb=" CG1 ILE B  43 "
            pdb=" CG2 ILE B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1121 not shown)

  Planarity restraints: 1216
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.038 5.00e-02 4.00e+02   5.74e-02 5.27e+00
        pdb=" N   PRO B 236 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 328 "    0.011 2.00e-02 2.50e+03   2.26e-02 5.13e+00
        pdb=" C   TYR R 328 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   TYR R 328 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR R 329 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 182 "    0.035 5.00e-02 4.00e+02   5.33e-02 4.55e+00
        pdb=" N   PRO R 183 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO R 183 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO R 183 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1213 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1929
        2.82 -     3.34: 6335
        3.34 -     3.86: 11222
        3.86 -     4.38: 12432
        4.38 -     4.90: 22331
  Nonbonded interactions: 54249
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.298 2.440
  nonbonded pdb=" O   ALA R 325 "
            pdb=" OG1 THR R 329 "
     model   vdw
     2.304 2.440
  nonbonded pdb=" OG1 THR B  34 "
            pdb=" O   LEU B 300 "
     model   vdw
     2.314 2.440
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.315 2.440
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" O   LYS A 277 "
     model   vdw
     2.334 2.440
  ... (remaining 54244 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.770
  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:          3.860
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     21.420
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  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:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
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      :  0.004   0.038   7186  Z= 0.238
  Angle     :  0.813  11.310   9728  Z= 0.453
  Chirality :  0.053   0.284   1124
  Planarity :  0.006   0.057   1216
  Dihedral  :  8.642  75.491   2581
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.24), residues: 877
  helix: -0.65 (0.21), residues: 367
  sheet:  0.10 (0.41), residues: 159
  loop : -1.85 (0.27), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.016   0.002   PHE A 274 
 TYR   0.023   0.002   TYR R 151 
 ARG   0.004   0.000   ARG A  24 

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: B  155 ASN cc_start: 0.7455 (m-40) cc_final: 0.6985 (t0)
REVERT: B  259 GLN cc_start: 0.7799 (pt0) cc_final: 0.7502 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1925
  time to fit residues: 48.6027
Evaluate side-chains
  110 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:    7.9990
   chunk 65 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
B 119 ASN
** R 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 190 ASN
R 193 ASN
R 299 HIS
R 330 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7186  Z= 0.281
  Angle     :  0.592  13.764   9728  Z= 0.306
  Chirality :  0.042   0.207   1124
  Planarity :  0.004   0.041   1216
  Dihedral  :  4.245  20.323    962
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  :  9.96 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -0.06 (0.27), residues: 877
  helix:  1.13 (0.25), residues: 376
  sheet:  0.19 (0.41), residues: 159
  loop : -1.48 (0.29), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  99 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.014   0.001   PHE B 241 
 TYR   0.020   0.002   TYR R 229 
 ARG   0.004   0.000   ARG A 313 

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A  210 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7285 (mtmt)
REVERT: B  155 ASN cc_start: 0.7507 (m-40) cc_final: 0.7090 (t0)
REVERT: B  220 GLN cc_start: 0.8262 (mp10) cc_final: 0.8008 (mp10)
REVERT: R  190 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.8084 (m-40)
  outliers start: 23
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1721
  time to fit residues: 35.6429
Evaluate side-chains
  131 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  210 LYS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  190 ASN
Chi-restraints excluded: chain R residue  216 SER
Chi-restraints excluded: chain R residue  292 ILE
Chi-restraints excluded: chain R residue  336 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   chunk 70 optimal weight:    0.1980
   chunk 78 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 185 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7186  Z= 0.262
  Angle     :  0.549   9.571   9728  Z= 0.287
  Chirality :  0.042   0.175   1124
  Planarity :  0.003   0.039   1216
  Dihedral  :  4.066  16.951    962
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 11.90 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.34 (0.28), residues: 877
  helix:  1.56 (0.26), residues: 382
  sheet:  0.14 (0.39), residues: 167
  loop : -1.34 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  99 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.013   0.001   PHE B 241 
 TYR   0.020   0.002   TYR R 151 
 ARG   0.004   0.000   ARG B 304 

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 115
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7673 (ptpp)
REVERT: B  124 TYR cc_start: 0.8686 (m-80) cc_final: 0.7854 (m-80)
REVERT: B  220 GLN cc_start: 0.8312 (mp10) cc_final: 0.7868 (mp10)
  outliers start: 34
  outliers final: 25
  residues processed: 136
  average time/residue: 0.1598
  time to fit residues: 30.2720
Evaluate side-chains
  134 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue   99 THR
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  164 SER
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  292 ILE
Chi-restraints excluded: chain R residue  336 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.3832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   7186  Z= 0.354
  Angle     :  0.595   8.200   9728  Z= 0.311
  Chirality :  0.043   0.164   1124
  Planarity :  0.004   0.044   1216
  Dihedral  :  4.247  17.036    962
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 12.55 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.35 (0.28), residues: 877
  helix:  1.63 (0.27), residues: 375
  sheet: -0.45 (0.39), residues: 176
  loop : -0.98 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  99 
 HIS   0.007   0.001   HIS B  62 
 PHE   0.015   0.002   PHE B 241 
 TYR   0.023   0.003   TYR B 289 
 ARG   0.007   0.000   ARG A 313 

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 117
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  302 TYR cc_start: 0.8307 (t80) cc_final: 0.7630 (t80)
REVERT: B  124 TYR cc_start: 0.8812 (m-80) cc_final: 0.8604 (m-80)
REVERT: B  138 GLU cc_start: 0.7889 (tp30) cc_final: 0.7687 (tp30)
REVERT: B  198 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7468 (pp)
REVERT: B  220 GLN cc_start: 0.8313 (mp10) cc_final: 0.8067 (mp10)
REVERT: R  232 ASN cc_start: 0.7604 (m-40) cc_final: 0.7391 (m-40)
  outliers start: 40
  outliers final: 32
  residues processed: 144
  average time/residue: 0.1732
  time to fit residues: 34.4348
Evaluate side-chains
  142 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 109
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue   99 THR
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  111 ASN
Chi-restraints excluded: chain R residue  164 SER
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  227 THR
Chi-restraints excluded: chain R residue  292 ILE
Chi-restraints excluded: chain R residue  336 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 47 optimal weight:    0.0570
   chunk 1 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 58 optimal weight:    0.1980
   chunk 0 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.5500

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7186  Z= 0.182
  Angle     :  0.500   7.556   9728  Z= 0.262
  Chirality :  0.040   0.145   1124
  Planarity :  0.003   0.042   1216
  Dihedral  :  3.944  17.096    962
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 15.01 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.59 (0.29), residues: 877
  helix:  1.90 (0.27), residues: 376
  sheet: -0.31 (0.39), residues: 171
  loop : -0.98 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 297 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.013   0.001   PHE R  89 
 TYR   0.018   0.001   TYR R 151 
 ARG   0.006   0.000   ARG A 313 

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 116
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
REVERT: A  302 TYR cc_start: 0.8267 (t80) cc_final: 0.7560 (t80)
REVERT: A  317 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7603 (ptpp)
REVERT: B  124 TYR cc_start: 0.8597 (m-80) cc_final: 0.7666 (m-80)
REVERT: B  127 LYS cc_start: 0.7803 (mptt) cc_final: 0.7561 (mptt)
REVERT: B  188 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6628 (mtp)
REVERT: B  220 GLN cc_start: 0.8201 (mp10) cc_final: 0.7965 (mp10)
REVERT: B  263 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8320 (m)
  outliers start: 34
  outliers final: 23
  residues processed: 142
  average time/residue: 0.1705
  time to fit residues: 33.4152
Evaluate side-chains
  134 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  227 THR
Chi-restraints excluded: chain R residue  292 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 6 optimal weight:    0.6980
   chunk 27 optimal weight:    0.3980
   chunk 44 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 126 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.3905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7186  Z= 0.193
  Angle     :  0.507   9.479   9728  Z= 0.262
  Chirality :  0.040   0.148   1124
  Planarity :  0.003   0.042   1216
  Dihedral  :  3.869  15.936    962
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 16.30 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.70 (0.29), residues: 877
  helix:  2.00 (0.27), residues: 376
  sheet: -0.25 (0.39), residues: 171
  loop : -0.95 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.002   0.001   HIS B  62 
 PHE   0.008   0.001   PHE B 241 
 TYR   0.020   0.002   TYR B  85 
 ARG   0.007   0.000   ARG A 313 

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
REVERT: A  302 TYR cc_start: 0.8313 (t80) cc_final: 0.7686 (t80)
REVERT: A  317 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7577 (ptpp)
REVERT: B  124 TYR cc_start: 0.8637 (m-80) cc_final: 0.7681 (m-80)
REVERT: B  127 LYS cc_start: 0.7765 (mptt) cc_final: 0.7543 (mptt)
REVERT: B  188 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6634 (mtp)
REVERT: B  220 GLN cc_start: 0.8209 (mp10) cc_final: 0.7976 (mp10)
REVERT: B  263 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8315 (m)
  outliers start: 31
  outliers final: 24
  residues processed: 136
  average time/residue: 0.1695
  time to fit residues: 32.0400
Evaluate side-chains
  134 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  164 SER
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  227 THR
Chi-restraints excluded: chain R residue  292 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 47 optimal weight:    0.1980
   chunk 61 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
R 330 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.3985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7186  Z= 0.196
  Angle     :  0.512   8.675   9728  Z= 0.264
  Chirality :  0.040   0.144   1124
  Planarity :  0.003   0.042   1216
  Dihedral  :  3.845  15.852    962
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 18.11 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.76 (0.29), residues: 877
  helix:  2.08 (0.27), residues: 375
  sheet: -0.23 (0.39), residues: 171
  loop : -0.94 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.017   0.002   TYR B  85 
 ARG   0.007   0.000   ARG A 313 

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
REVERT: A  302 TYR cc_start: 0.8335 (t80) cc_final: 0.7721 (t80)
REVERT: A  317 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7572 (ptpp)
REVERT: B  124 TYR cc_start: 0.8644 (m-80) cc_final: 0.7673 (m-80)
REVERT: B  127 LYS cc_start: 0.7778 (mptt) cc_final: 0.7566 (mptt)
REVERT: B  188 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6660 (mtp)
REVERT: B  220 GLN cc_start: 0.8190 (mp10) cc_final: 0.7926 (mp10)
REVERT: B  263 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8298 (m)
  outliers start: 31
  outliers final: 25
  residues processed: 136
  average time/residue: 0.1699
  time to fit residues: 31.9783
Evaluate side-chains
  135 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue   99 THR
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  164 SER
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  227 THR
Chi-restraints excluded: chain R residue  292 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 57 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 78 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** R 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.4093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7186  Z= 0.204
  Angle     :  0.517   9.137   9728  Z= 0.267
  Chirality :  0.040   0.145   1124
  Planarity :  0.003   0.042   1216
  Dihedral  :  3.850  15.531    962
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 18.76 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.72 (0.29), residues: 877
  helix:  2.08 (0.28), residues: 374
  sheet: -0.30 (0.39), residues: 173
  loop : -0.96 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.011   0.001   PHE R  89 
 TYR   0.019   0.002   TYR B  85 
 ARG   0.007   0.000   ARG A 313 

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
REVERT: A  302 TYR cc_start: 0.8306 (t80) cc_final: 0.7829 (t80)
REVERT: A  317 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7549 (ptpp)
REVERT: A  318 GLU cc_start: 0.7642 (pm20) cc_final: 0.7155 (mm-30)
REVERT: B  124 TYR cc_start: 0.8647 (m-80) cc_final: 0.7657 (m-80)
REVERT: B  127 LYS cc_start: 0.7793 (mptt) cc_final: 0.7544 (mptt)
REVERT: B  188 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6679 (mtp)
REVERT: B  220 GLN cc_start: 0.8220 (mp10) cc_final: 0.7930 (mp10)
REVERT: B  263 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8347 (m)
  outliers start: 30
  outliers final: 26
  residues processed: 134
  average time/residue: 0.1690
  time to fit residues: 31.6381
Evaluate side-chains
  136 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue   99 THR
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  164 SER
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  227 THR
Chi-restraints excluded: chain R residue  292 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 23 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 77 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 57 optimal weight:    0.3980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
R 126 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.4216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7186  Z= 0.222
  Angle     :  0.529   9.757   9728  Z= 0.274
  Chirality :  0.041   0.146   1124
  Planarity :  0.003   0.042   1216
  Dihedral  :  3.871  15.258    962
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 19.28 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.70 (0.29), residues: 877
  helix:  2.09 (0.27), residues: 374
  sheet: -0.35 (0.39), residues: 175
  loop : -0.97 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.010   0.001   PHE R  89 
 TYR   0.019   0.002   TYR B  85 
 ARG   0.007   0.000   ARG A 313 

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
REVERT: A  302 TYR cc_start: 0.8317 (t80) cc_final: 0.7819 (t80)
REVERT: A  317 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7526 (ptpp)
REVERT: A  318 GLU cc_start: 0.7705 (pm20) cc_final: 0.7198 (mm-30)
REVERT: B  124 TYR cc_start: 0.8665 (m-80) cc_final: 0.7702 (m-80)
REVERT: B  127 LYS cc_start: 0.7781 (mptt) cc_final: 0.7515 (mptt)
REVERT: B  188 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6730 (mtp)
REVERT: B  220 GLN cc_start: 0.8221 (mp10) cc_final: 0.7954 (mp10)
REVERT: B  263 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8291 (m)
  outliers start: 32
  outliers final: 25
  residues processed: 133
  average time/residue: 0.1597
  time to fit residues: 29.5399
Evaluate side-chains
  136 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue   99 THR
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  164 SER
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  227 THR
Chi-restraints excluded: chain R residue  292 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.4566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   7186  Z= 0.391
  Angle     :  0.620   9.213   9728  Z= 0.323
  Chirality :  0.043   0.150   1124
  Planarity :  0.004   0.044   1216
  Dihedral  :  4.279  16.739    962
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 19.02 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.36 (0.29), residues: 877
  helix:  1.82 (0.27), residues: 373
  sheet: -0.79 (0.39), residues: 172
  loop : -0.99 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B  62 
 PHE   0.014   0.002   PHE B 241 
 TYR   0.034   0.002   TYR B  85 
 ARG   0.007   0.000   ARG A 313 

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 ASP cc_start: 0.8375 (m-30) cc_final: 0.8102 (t0)
REVERT: A  302 TYR cc_start: 0.8358 (t80) cc_final: 0.7850 (t80)
REVERT: A  317 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7673 (ptpp)
REVERT: B  124 TYR cc_start: 0.8834 (m-80) cc_final: 0.7968 (m-80)
REVERT: B  127 LYS cc_start: 0.7821 (mptt) cc_final: 0.7599 (mptt)
REVERT: B  188 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6869 (mtp)
REVERT: B  263 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8286 (m)
  outliers start: 33
  outliers final: 25
  residues processed: 138
  average time/residue: 0.1778
  time to fit residues: 33.4760
Evaluate side-chains
  139 residues out of total 774 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 GLU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  306 GLN
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  327 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  230 ASN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue   99 THR
Chi-restraints excluded: chain R residue  103 THR
Chi-restraints excluded: chain R residue  164 SER
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  227 THR
Chi-restraints excluded: chain R residue  292 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 69 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0170
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 46 optimal weight:    0.3980
   overall best weight:    0.4418

-------------------------------------------------------------------------------
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 = 0.4211 r_free = 0.4211 target = 0.197300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.153696 restraints weight = 7585.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 2.21
r_work: 0.3589 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.4388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7186  Z= 0.170
  Angle     :  0.527   9.227   9728  Z= 0.270
  Chirality :  0.040   0.160   1124
  Planarity :  0.003   0.042   1216
  Dihedral  :  3.927  16.393    962
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.05 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.64 (0.29), residues: 877
  helix:  2.07 (0.28), residues: 375
  sheet: -0.38 (0.41), residues: 157
  loop : -1.04 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 297 
 HIS   0.002   0.001   HIS B  54 
 PHE   0.008   0.001   PHE B 241 
 TYR   0.017   0.001   TYR R 151 
 ARG   0.006   0.000   ARG A 313 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1845.14 seconds
wall clock time: 34 minutes 18.28 seconds (2058.28 seconds total)