Starting phenix.real_space_refine
on Tue Jul 29 22:31:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rpx_24625/07_2025/7rpx_24625.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rpx_24625/07_2025/7rpx_24625.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rpx_24625/07_2025/7rpx_24625.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rpx_24625/07_2025/7rpx_24625.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rpx_24625/07_2025/7rpx_24625.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rpx_24625/07_2025/7rpx_24625.cif"
  }
  resolution = 4.2
  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=   0.002 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Mn      3      7.51       5
     P      62      5.49       5
     S      32      5.16       5
     C    7302      2.51       5
     N    1944      2.21       5
     O    2411      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11754
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1945
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 8, 'TRANS': 242}
    Chain: "B"
      Number of atoms: 1922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1922
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 9, 'TRANS': 233}
    Chain: "C"
      Number of atoms: 1926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1926
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 5, 'TRANS': 237}
    Chain: "X"
      Number of atoms: 637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 637
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "Z"
      Number of atoms: 634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 634
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "E"
      Number of atoms: 4687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 590, 4687
          Classifications: {'peptide': 590}
          Link IDs: {'PTRANS': 21, 'TRANS': 568}
    Chain: "X"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 7.33, per 1000 atoms: 0.62
  Number of scatterers: 11754
  At special positions: 0
  Unit cell: (114, 108, 120, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      3     24.99
     S      32     16.00
     P      62     15.00
     O    2411      8.00
     N    1944      7.00
     C    7302      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.61
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2496

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 15 sheets defined
      26.0% alpha, 19.4% beta
      30 base pairs and 47 stacking pairs defined.
    Time for finding SS restraints: 4.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 21
    Processing helix  chain 'A' and resid 74 through 79
    Processing helix  chain 'A' and resid 142 through 154
      removed outlier: 4.351A  pdb=" N   LEU A 152 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   VAL A 153 " --> pdb=" O   ASP A 149 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY A 154 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 210
    Processing helix  chain 'A' and resid 211 through 213
      No H-bonds generated for 'chain 'A' and resid 211 through 213'
    Processing helix  chain 'B' and resid 7 through 17
      removed outlier: 3.973A  pdb=" N   SER B  12 " --> pdb=" O   ALA B   8 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   TYR B  13 " --> pdb=" O   VAL B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 20
      No H-bonds generated for 'chain 'B' and resid 18 through 20'
    Processing helix  chain 'B' and resid 71 through 78
    Processing helix  chain 'B' and resid 79 through 81
      No H-bonds generated for 'chain 'B' and resid 79 through 81'
    Processing helix  chain 'B' and resid 136 through 147
      removed outlier: 4.263A  pdb=" N   ALA B 140 " --> pdb=" O   THR B 136 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ASP B 141 " --> pdb=" O   ILE B 137 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLU B 145 " --> pdb=" O   ASP B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 203
      removed outlier: 3.502A  pdb=" N   ASN B 203 " --> pdb=" O   GLU B 199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 14
    Processing helix  chain 'C' and resid 15 through 20
      removed outlier: 4.445A  pdb=" N   ARG C  20 " --> pdb=" O   GLN C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 77
    Processing helix  chain 'C' and resid 135 through 147
      removed outlier: 3.877A  pdb=" N   SER C 147 " --> pdb=" O   ILE C 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 202
    Processing helix  chain 'C' and resid 204 through 211
      removed outlier: 3.842A  pdb=" N   LEU C 207 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   THR C 208 " --> pdb=" O   LEU C 205 " (cutoff:3.500A)
      removed outlier: 5.585A  pdb=" N   LYS C 209 " --> pdb=" O   SER C 206 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU C 210 " --> pdb=" O   LEU C 207 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 4 through 9
    Processing helix  chain 'E' and resid 21 through 30
      removed outlier: 4.054A  pdb=" N   LEU E  30 " --> pdb=" O   LEU E  26 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 35 through 42
      removed outlier: 4.242A  pdb=" N   ASP E  39 " --> pdb=" O   LYS E  35 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 43 through 47
      removed outlier: 3.572A  pdb=" N   GLN E  46 " --> pdb=" O   TYR E  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 74
    Processing helix  chain 'E' and resid 77 through 89
      removed outlier: 4.191A  pdb=" N   VAL E  81 " --> pdb=" O   ASP E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 94 through 99
    Processing helix  chain 'E' and resid 120 through 134
      removed outlier: 3.508A  pdb=" N   LEU E 133 " --> pdb=" O   SER E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 139 through 153
      removed outlier: 3.559A  pdb=" N   LEU E 146 " --> pdb=" O   LEU E 142 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU E 147 " --> pdb=" O   LYS E 143 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 161 through 168
      removed outlier: 3.530A  pdb=" N   VAL E 166 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 175 through 187
      removed outlier: 3.677A  pdb=" N   VAL E 179 " --> pdb=" O   GLY E 175 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASP E 181 " --> pdb=" O   ALA E 177 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ALA E 184 " --> pdb=" O   LEU E 180 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 192
      No H-bonds generated for 'chain 'E' and resid 190 through 192'
    Processing helix  chain 'E' and resid 193 through 204
      removed outlier: 4.203A  pdb=" N   LEU E 203 " --> pdb=" O   ARG E 199 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   ARG E 204 " --> pdb=" O   ALA E 200 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 208 through 217
    Processing helix  chain 'E' and resid 218 through 223
    Processing helix  chain 'E' and resid 289 through 297
      removed outlier: 4.047A  pdb=" N   VAL E 293 " --> pdb=" O   TYR E 289 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ASP E 294 " --> pdb=" O   PRO E 290 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   TYR E 295 " --> pdb=" O   ASP E 291 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 323 through 328
    Processing helix  chain 'E' and resid 329 through 332
      removed outlier: 4.015A  pdb=" N   ARG E 332 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 329 through 332'
    Processing helix  chain 'E' and resid 335 through 340
      removed outlier: 3.631A  pdb=" N   ALA E 339 " --> pdb=" O   ASP E 335 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE E 340 " --> pdb=" O   ILE E 336 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 335 through 340'
    Processing helix  chain 'E' and resid 392 through 398
      removed outlier: 3.743A  pdb=" N   LYS E 397 " --> pdb=" O   GLU E 394 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   SER E 398 " --> pdb=" O   ASP E 395 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 399 through 404
    Processing helix  chain 'E' and resid 490 through 504
      removed outlier: 3.764A  pdb=" N   GLN E 498 " --> pdb=" O   LEU E 494 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LYS E 499 " --> pdb=" O   ASP E 495 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 570 through 574
    Processing helix  chain 'E' and resid 576 through 587
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6
      removed outlier: 3.604A  pdb=" N   ILE A   4 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LYS A 110 " --> pdb=" O   GLU C 175 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27
    Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31
      removed outlier: 3.527A  pdb=" N   ARG A  51 " --> pdb=" O   HIS A 240 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL A 233 " --> pdb=" O   MET A 241 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   PHE A 243 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE A 231 " --> pdb=" O   PHE A 243 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ILE A 245 " --> pdb=" O   MET A 229 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   MET A 229 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   GLY A 224 " --> pdb=" O   PRO A 228 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL A 134 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201
      removed outlier: 4.155A  pdb=" N   MET A 157 " --> pdb=" O   TYR A 200 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ALA A 179 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ALA A 170 " --> pdb=" O   TYR A 177 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   TYR A 177 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 178 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5
      removed outlier: 4.011A  pdb=" N   LEU B  88 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 67
      removed outlier: 3.868A  pdb=" N   GLU B  66 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ASN B  26 " --> pdb=" O   SER B  37 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   SER B  37 " --> pdb=" O   ASN B  26 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE B  28 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ILE B  34 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU B  47 " --> pdb=" O   GLY B  38 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ASP B  48 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ASP B 237 " --> pdb=" O   ASP B  48 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   SER B 213 " --> pdb=" O   LYS B 229 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU B 216 " --> pdb=" O   ALA B 132 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 193 through 197
      removed outlier: 3.681A  pdb=" N   ILE B 155 " --> pdb=" O   SER B 194 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   VAL B 152 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE B 167 " --> pdb=" O   VAL B 152 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   HIS B 156 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TYR B 163 " --> pdb=" O   HIS B 156 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLU C 108 " --> pdb=" O   LYS B 174 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ARG C 107 " --> pdb=" O   ILE C 101 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   VAL C 111 " --> pdb=" O   VAL C  97 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLU C  58 " --> pdb=" O   VAL C   4 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 29
      removed outlier: 3.835A  pdb=" N   LYS C  28 " --> pdb=" O   GLU C  35 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 163 through 165
    Processing sheet with id=AB1, first strand: chain 'E' and resid 256 through 257
      removed outlier: 3.601A  pdb=" N   VAL E 257 " --> pdb=" O   ILE E 388 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE E 388 " --> pdb=" O   VAL E 257 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'E' and resid 265 through 266
      removed outlier: 6.621A  pdb=" N   GLU E 308 " --> pdb=" O   PHE E 350 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL E 312 " --> pdb=" O   ASN E 346 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   LYS E 383 " --> pdb=" O   VAL E 345 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   VAL E 347 " --> pdb=" O   LYS E 383 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 354 through 355
      removed outlier: 3.828A  pdb=" N   TYR E 355 " --> pdb=" O   VAL E 358 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 505 through 506
      removed outlier: 3.818A  pdb=" N   TRP E 522 " --> pdb=" O   ARG E 506 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ILE E 521 " --> pdb=" O   GLY E 453 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   GLY E 453 " --> pdb=" O   ILE E 521 " (cutoff:3.500A)
      removed outlier: 5.077A  pdb=" N   VAL E 451 " --> pdb=" O   VAL E 523 " (cutoff:3.500A)
      removed outlier: 9.952A  pdb=" N   LEU E 448 " --> pdb=" O   TYR E 472 " (cutoff:3.500A)
      removed outlier: 8.470A  pdb=" N   TYR E 472 " --> pdb=" O   LEU E 448 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   VAL E 450 " --> pdb=" O   ALA E 470 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ALA E 470 " --> pdb=" O   VAL E 450 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY E 452 " --> pdb=" O   LEU E 468 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   CYS E 483 " --> pdb=" O   MET E 469 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   ALA E 471 " --> pdb=" O   SER E 481 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   SER E 481 " --> pdb=" O   ALA E 471 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ASN E 473 " --> pdb=" O   PHE E 479 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   PHE E 479 " --> pdb=" O   ASN E 473 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   PHE E 479 " --> pdb=" O   ASN E 514 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 505 through 506
      removed outlier: 3.818A  pdb=" N   TRP E 522 " --> pdb=" O   ARG E 506 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ILE E 521 " --> pdb=" O   GLY E 453 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   GLY E 453 " --> pdb=" O   ILE E 521 " (cutoff:3.500A)
      removed outlier: 5.077A  pdb=" N   VAL E 451 " --> pdb=" O   VAL E 523 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG E 564 " --> pdb=" O   GLU E 530 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   ILE E 532 " --> pdb=" O   PHE E 562 " (cutoff:3.500A)
      removed outlier: 5.227A  pdb=" N   PHE E 562 " --> pdb=" O   ILE E 532 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 536 through 539

    311 hydrogen bonds defined for protein.
    834 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      77 hydrogen bonds
      154 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      47 stacking parallelities
  Total time for adding SS restraints: 3.96

  Time building geometry restraints manager: 3.20 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: 3508
        1.34 -     1.46: 2187
        1.46 -     1.58: 6196
        1.58 -     1.70: 122
        1.70 -     1.82: 61
  Bond restraints: 12074
  Sorted by residual:
  bond pdb=" N   MET A 182 "
       pdb=" CA  MET A 182 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.034 1.31e-02 5.83e+03 6.89e+00
  bond pdb=" N   LYS A 183 "
       pdb=" CA  LYS A 183 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.032 1.29e-02 6.01e+03 6.35e+00
  bond pdb=" N   ASP A 184 "
       pdb=" CA  ASP A 184 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 5.99e+00
  bond pdb=" N   LEU A 187 "
       pdb=" CA  LEU A 187 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.29e-02 6.01e+03 5.41e+00
  bond pdb=" N   LYS A 185 "
       pdb=" CA  LYS A 185 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.41e-02 5.03e+03 4.72e+00
  ... (remaining 12069 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 16346
        2.12 -     4.24: 188
        4.24 -     6.37: 10
        6.37 -     8.49: 1
        8.49 -    10.61: 2
  Bond angle restraints: 16547
  Sorted by residual:
  angle pdb=" CA  MET A 182 "
        pdb=" C   MET A 182 "
        pdb=" O   MET A 182 "
      ideal   model   delta    sigma   weight residual
     121.47  116.61    4.86 1.15e+00 7.56e-01 1.79e+01
  angle pdb=" OP1  DG X  25 "
        pdb=" P    DG X  25 "
        pdb=" OP2  DG X  25 "
      ideal   model   delta    sigma   weight residual
     120.00  109.39   10.61 3.00e+00 1.11e-01 1.25e+01
  angle pdb=" O   MET A 182 "
        pdb=" C   MET A 182 "
        pdb=" N   LYS A 183 "
      ideal   model   delta    sigma   weight residual
     122.96  126.60   -3.64 1.13e+00 7.83e-01 1.04e+01
  angle pdb=" N   GLY E 173 "
        pdb=" CA  GLY E 173 "
        pdb=" C   GLY E 173 "
      ideal   model   delta    sigma   weight residual
     115.63  111.19    4.44 1.49e+00 4.50e-01 8.89e+00
  angle pdb=" N   ASP A  55 "
        pdb=" CA  ASP A  55 "
        pdb=" C   ASP A  55 "
      ideal   model   delta    sigma   weight residual
     114.56  110.82    3.74 1.27e+00 6.20e-01 8.69e+00
  ... (remaining 16542 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.28: 6865
       32.28 -    64.57: 335
       64.57 -    96.85: 4
       96.85 -   129.13: 0
      129.13 -   161.42: 2
  Dihedral angle restraints: 7206
    sinusoidal: 3343
      harmonic: 3863
  Sorted by residual:
  dihedral pdb=" C4'  DA Z  22 "
           pdb=" C3'  DA Z  22 "
           pdb=" O3'  DA Z  22 "
           pdb=" P    DC Z  23 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   58.58  161.42     1      3.50e+01 8.16e-04 1.53e+01
  dihedral pdb=" C4'  DA Z  16 "
           pdb=" C3'  DA Z  16 "
           pdb=" O3'  DA Z  16 "
           pdb=" P    DG Z  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   71.96  148.04     1      3.50e+01 8.16e-04 1.45e+01
  dihedral pdb=" CA  PHE C  69 "
           pdb=" C   PHE C  69 "
           pdb=" N   ASN C  70 "
           pdb=" CA  ASN C  70 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.69   17.31     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 7203 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 1749
       0.079 -    0.157: 145
       0.157 -    0.236: 1
       0.236 -    0.315: 0
       0.315 -    0.393: 1
  Chirality restraints: 1896
  Sorted by residual:
  chirality pdb=" P    DG X  25 "
            pdb=" OP1  DG X  25 "
            pdb=" OP2  DG X  25 "
            pdb=" O5'  DG X  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.74   -0.39 2.00e-01 2.50e+01 3.87e+00
  chirality pdb=" CA  PRO A 186 "
            pdb=" N   PRO A 186 "
            pdb=" C   PRO A 186 "
            pdb=" CB  PRO A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.92   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  ILE E 233 "
            pdb=" N   ILE E 233 "
            pdb=" C   ILE E 233 "
            pdb=" CB  ILE E 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.88e-01
  ... (remaining 1893 not shown)

  Planarity restraints: 1892
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 121 "    0.034 5.00e-02 4.00e+02   5.08e-02 4.12e+00
        pdb=" N   PRO B 122 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO B 122 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 122 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 181 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.76e+00
        pdb=" C   LEU A 181 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LEU A 181 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   MET A 182 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 226 "   -0.025 5.00e-02 4.00e+02   3.72e-02 2.22e+00
        pdb=" N   PRO E 227 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO E 227 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO E 227 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1889 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.30: 32
        2.30 -     2.95: 5427
        2.95 -     3.60: 17388
        3.60 -     4.25: 26869
        4.25 -     4.90: 42757
  Nonbonded interactions: 92473
  Sorted by model distance:
  nonbonded pdb=" O   GLY E  60 "
            pdb="MN    MN E 701 "
     model   vdw
     1.655 2.320
  nonbonded pdb=" OP1  DG X  22 "
            pdb="MN    MN X 101 "
     model   vdw
     1.753 2.320
  nonbonded pdb=" O   GLU E 167 "
            pdb="MN    MN E 702 "
     model   vdw
     1.770 2.320
  nonbonded pdb=" N   GLY E  62 "
            pdb="MN    MN E 701 "
     model   vdw
     1.887 2.400
  nonbonded pdb=" C   ILE E  61 "
            pdb="MN    MN E 701 "
     model   vdw
     1.940 2.550
  ... (remaining 92468 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     31.420
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6087
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   0.049  12074  Z= 0.155
  Angle     :  0.556  10.609  16547  Z= 0.311
  Chirality :  0.042   0.393   1896
  Planarity :  0.003   0.051   1892
  Dihedral  : 15.951 161.418   4710
  Min Nonbonded Distance : 1.655

Molprobity Statistics.
  All-atom Clashscore : 21.85
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.87 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  9.00 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.44 (0.23), residues: 1319
  helix: -0.91 (0.31), residues: 294
  sheet: -0.63 (0.31), residues: 332
  loop : -2.53 (0.22), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 431 
 HIS   0.002   0.001   HIS B 156 
 PHE   0.014   0.001   PHE B 101 
 TYR   0.022   0.001   TYR C 200 
 ARG   0.002   0.000   ARG E 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25909 (  386)
  hydrogen bonds       : angle       9.68139 (  988)
  covalent geometry    : bond        0.00306 (12074)
  covalent geometry    : angle       0.55619 (16547)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 294
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.7372 (t80) cc_final: 0.7117 (t80)
REVERT: A   24 ASP cc_start: 0.6700 (t0) cc_final: 0.6020 (t0)
REVERT: A   26 ILE cc_start: 0.8107 (pt) cc_final: 0.7893 (pt)
REVERT: A   29 ASN cc_start: 0.6231 (m-40) cc_final: 0.5651 (m110)
REVERT: A   30 PHE cc_start: 0.8159 (m-80) cc_final: 0.7950 (m-80)
REVERT: A   69 LYS cc_start: 0.7697 (tppt) cc_final: 0.7480 (tppt)
REVERT: A   86 LYS cc_start: 0.8023 (pttp) cc_final: 0.7307 (pptt)
REVERT: A  164 ASP cc_start: 0.7677 (t0) cc_final: 0.5804 (t0)
REVERT: A  182 MET cc_start: 0.4462 (mmm) cc_final: 0.4132 (mmm)
REVERT: A  183 LYS cc_start: 0.8935 (tttt) cc_final: 0.8655 (mmtm)
REVERT: A  210 LYS cc_start: 0.8803 (ptmt) cc_final: 0.8307 (ptpt)
REVERT: A  213 ARG cc_start: 0.5305 (OUTLIER) cc_final: 0.4583 (mpp80)
REVERT: A  232 ASP cc_start: 0.6464 (t0) cc_final: 0.6006 (t0)
REVERT: A  244 TRP cc_start: 0.7138 (m100) cc_final: 0.6773 (m100)
REVERT: B   11 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.6347 (t80)
REVERT: B   16 ARG cc_start: 0.7724 (mtm180) cc_final: 0.7434 (ttm-80)
REVERT: B   55 TYR cc_start: 0.4681 (OUTLIER) cc_final: 0.1756 (t80)
REVERT: B   68 ILE cc_start: 0.8603 (mt) cc_final: 0.8101 (mm)
REVERT: B  156 HIS cc_start: 0.6875 (p90) cc_final: 0.6503 (p-80)
REVERT: B  191 ASP cc_start: 0.7241 (m-30) cc_final: 0.6496 (m-30)
REVERT: C   70 ASN cc_start: 0.4626 (t0) cc_final: 0.4310 (t0)
REVERT: C   83 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7831 (mpp80)
REVERT: C  128 PHE cc_start: 0.6684 (m-80) cc_final: 0.4537 (m-10)
REVERT: C  165 LYS cc_start: 0.6958 (pttp) cc_final: 0.6606 (pttp)
REVERT: E  145 ARG cc_start: 0.5175 (OUTLIER) cc_final: 0.4526 (ttm-80)
REVERT: E  162 LEU cc_start: 0.7773 (mt) cc_final: 0.7253 (mt)
REVERT: E  213 ILE cc_start: 0.8145 (mt) cc_final: 0.7721 (mt)
REVERT: E  303 LYS cc_start: 0.8829 (mptp) cc_final: 0.8517 (mmtm)
REVERT: E  454 PHE cc_start: 0.5176 (m-80) cc_final: 0.3298 (m-80)
REVERT: E  517 MET cc_start: 0.5501 (ttm) cc_final: 0.5172 (ttm)
REVERT: E  583 MET cc_start: 0.8854 (mtp) cc_final: 0.8508 (mtp)
  outliers start: 10
  outliers final: 2
  residues processed: 302
  average time/residue: 0.3229
  time to fit residues: 127.1675
Evaluate side-chains
  221 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 215
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    0.0000
   chunk 104 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 55 optimal weight:    0.4980
   chunk 108 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 125 optimal weight:    2.9990
   overall best weight:    1.0988

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

Flipped N/Q/H residues before XYZ refinement:
** C  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 288 GLN
E 386 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.187076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.157930 restraints weight = 23820.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.162525 restraints weight = 14536.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.165825 restraints weight = 9938.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4318
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4318 r_free = 0.4318    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4317 r_free = 0.4317    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.4317
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6115
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12074  Z= 0.181
  Angle     :  0.693   9.611  16547  Z= 0.371
  Chirality :  0.048   0.227   1896
  Planarity :  0.005   0.053   1892
  Dihedral  : 19.349 160.160   2087
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 16.45
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.46 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.54 %
    Favored  : 95.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.74 (0.22), residues: 1319
  helix: -1.31 (0.28), residues: 308
  sheet: -0.93 (0.29), residues: 337
  loop : -2.59 (0.22), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP E 431 
 HIS   0.002   0.001   HIS B 156 
 PHE   0.027   0.002   PHE E 400 
 TYR   0.023   0.002   TYR B  13 
 ARG   0.005   0.001   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05227 (  386)
  hydrogen bonds       : angle       7.05533 (  988)
  covalent geometry    : bond        0.00394 (12074)
  covalent geometry    : angle       0.69277 (16547)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 250
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.6680 (t0) cc_final: 0.5964 (t0)
REVERT: A  163 GLU cc_start: 0.8121 (tp30) cc_final: 0.7913 (mm-30)
REVERT: A  164 ASP cc_start: 0.7815 (t0) cc_final: 0.6331 (t0)
REVERT: A  165 LYS cc_start: 0.8683 (pttm) cc_final: 0.8048 (pttm)
REVERT: A  182 MET cc_start: 0.3872 (mmm) cc_final: 0.3627 (mmm)
REVERT: A  183 LYS cc_start: 0.9114 (tttt) cc_final: 0.8697 (mmtm)
REVERT: A  184 ASP cc_start: 0.7730 (t0) cc_final: 0.7263 (t0)
REVERT: A  185 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7860 (mmtm)
REVERT: A  210 LYS cc_start: 0.8821 (ptmt) cc_final: 0.8046 (ptpp)
REVERT: A  244 TRP cc_start: 0.7123 (m100) cc_final: 0.6602 (m100)
REVERT: B   59 PHE cc_start: 0.7587 (t80) cc_final: 0.7338 (t80)
REVERT: B  156 HIS cc_start: 0.6941 (p90) cc_final: 0.6476 (p-80)
REVERT: B  206 LYS cc_start: 0.8501 (ttmt) cc_final: 0.8266 (ttmm)
REVERT: B  213 SER cc_start: 0.6510 (t) cc_final: 0.6220 (p)
REVERT: C    2 LYS cc_start: 0.8161 (tptp) cc_final: 0.7894 (tppt)
REVERT: C   78 LEU cc_start: 0.7862 (mt) cc_final: 0.7599 (mt)
REVERT: C  165 LYS cc_start: 0.5443 (pttp) cc_final: 0.5154 (ptpp)
REVERT: C  230 MET cc_start: 0.0358 (mtp) cc_final: 0.0128 (mtp)
REVERT: E   99 LYS cc_start: 0.8160 (tttt) cc_final: 0.7855 (tttt)
REVERT: E  123 GLU cc_start: 0.6487 (tm-30) cc_final: 0.5877 (tm-30)
REVERT: E  160 LYS cc_start: 0.7566 (mttt) cc_final: 0.7065 (ptpp)
REVERT: E  180 LEU cc_start: 0.7570 (mt) cc_final: 0.7361 (mt)
REVERT: E  213 ILE cc_start: 0.8142 (mt) cc_final: 0.7937 (mt)
REVERT: E  303 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8701 (mmtm)
REVERT: E  304 GLU cc_start: 0.7550 (pm20) cc_final: 0.7196 (pm20)
REVERT: E  338 GLU cc_start: 0.7259 (tp30) cc_final: 0.7022 (tp30)
REVERT: E  342 GLU cc_start: 0.7276 (tp30) cc_final: 0.6779 (tm-30)
REVERT: E  583 MET cc_start: 0.8694 (mtp) cc_final: 0.8467 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 251
  average time/residue: 0.3096
  time to fit residues: 101.9621
Evaluate side-chains
  208 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 45 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 284 ASN
E 288 GLN
E 386 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.186956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.157667 restraints weight = 23810.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.162395 restraints weight = 14489.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.165695 restraints weight = 9841.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4319
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4319 r_free = 0.4319    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4319 r_free = 0.4319    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4319
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6128
moved from start:          0.3491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  12074  Z= 0.173
  Angle     :  0.664   9.536  16547  Z= 0.352
  Chirality :  0.046   0.202   1896
  Planarity :  0.004   0.053   1892
  Dihedral  : 19.312 162.106   2087
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.69 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  3.43 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.78 (0.22), residues: 1319
  helix: -1.26 (0.28), residues: 307
  sheet: -0.97 (0.29), residues: 339
  loop : -2.65 (0.22), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP E 431 
 HIS   0.002   0.001   HIS E 510 
 PHE   0.021   0.002   PHE B  27 
 TYR   0.021   0.002   TYR C 200 
 ARG   0.007   0.001   ARG C 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04567 (  386)
  hydrogen bonds       : angle       6.58712 (  988)
  covalent geometry    : bond        0.00387 (12074)
  covalent geometry    : angle       0.66397 (16547)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 236
  time to evaluate  : 1.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.6996 (t0) cc_final: 0.6256 (t0)
REVERT: A  163 GLU cc_start: 0.8178 (tp30) cc_final: 0.7949 (mm-30)
REVERT: A  164 ASP cc_start: 0.7953 (t0) cc_final: 0.6209 (t0)
REVERT: A  165 LYS cc_start: 0.8613 (pttm) cc_final: 0.8390 (pttm)
REVERT: A  182 MET cc_start: 0.3921 (mmm) cc_final: 0.3541 (mmm)
REVERT: A  183 LYS cc_start: 0.8636 (tttt) cc_final: 0.8380 (mmtm)
REVERT: B    1 MET cc_start: 0.5043 (ttm) cc_final: 0.4696 (tpp)
REVERT: B   59 PHE cc_start: 0.7514 (t80) cc_final: 0.7184 (t80)
REVERT: B   68 ILE cc_start: 0.8208 (mp) cc_final: 0.7723 (mp)
REVERT: B  156 HIS cc_start: 0.6775 (p90) cc_final: 0.6331 (p-80)
REVERT: B  158 LYS cc_start: 0.8174 (tptp) cc_final: 0.7874 (tppt)
REVERT: B  199 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7349 (tm-30)
REVERT: B  206 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8327 (ttmm)
REVERT: B  218 PHE cc_start: 0.8322 (t80) cc_final: 0.7280 (t80)
REVERT: C   78 LEU cc_start: 0.7903 (mt) cc_final: 0.7669 (mt)
REVERT: C  112 ARG cc_start: 0.7373 (ptm-80) cc_final: 0.6804 (ptm-80)
REVERT: C  153 VAL cc_start: 0.6118 (t) cc_final: 0.5898 (p)
REVERT: C  230 MET cc_start: 0.0222 (mtp) cc_final: -0.0092 (ttm)
REVERT: E   54 LEU cc_start: 0.8559 (mm) cc_final: 0.8247 (mt)
REVERT: E   99 LYS cc_start: 0.8134 (tttt) cc_final: 0.7864 (tttt)
REVERT: E  123 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6112 (tm-30)
REVERT: E  143 LYS cc_start: 0.7087 (mtmm) cc_final: 0.6773 (mtmm)
REVERT: E  258 ASP cc_start: 0.7196 (p0) cc_final: 0.6819 (p0)
REVERT: E  304 GLU cc_start: 0.7594 (pm20) cc_final: 0.7169 (pm20)
REVERT: E  338 GLU cc_start: 0.7191 (tp30) cc_final: 0.6584 (tp30)
REVERT: E  342 GLU cc_start: 0.7241 (tp30) cc_final: 0.6750 (tm-30)
REVERT: E  412 MET cc_start: 0.4043 (mmp) cc_final: 0.3450 (mmp)
REVERT: E  583 MET cc_start: 0.8690 (mtp) cc_final: 0.8469 (mtp)
  outliers start: 2
  outliers final: 0
  residues processed: 238
  average time/residue: 0.3238
  time to fit residues: 102.0911
Evaluate side-chains
  206 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 92 optimal weight:    0.0970
   chunk 119 optimal weight:    8.9990
   chunk 101 optimal weight:    4.9990
   chunk 103 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 498 GLN ** 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 = 0.4606 r_free = 0.4606 target = 0.190564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.160781 restraints weight = 23261.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.165537 restraints weight = 14082.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.168904 restraints weight = 9514.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.4335
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4339
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4339 r_free = 0.4339    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4339 r_free = 0.4339    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4339
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6098
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12074  Z= 0.152
  Angle     :  0.647   9.894  16547  Z= 0.341
  Chirality :  0.044   0.171   1896
  Planarity :  0.004   0.054   1892
  Dihedral  : 19.270 163.289   2087
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.92 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.26 %
    Favored  : 96.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.76 (0.22), residues: 1319
  helix: -1.24 (0.28), residues: 308
  sheet: -0.88 (0.29), residues: 330
  loop : -2.68 (0.22), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 431 
 HIS   0.002   0.001   HIS E 510 
 PHE   0.030   0.002   PHE B  27 
 TYR   0.023   0.002   TYR B 196 
 ARG   0.008   0.000   ARG C  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04129 (  386)
  hydrogen bonds       : angle       6.24855 (  988)
  covalent geometry    : bond        0.00338 (12074)
  covalent geometry    : angle       0.64703 (16547)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 230
  time to evaluate  : 1.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.7221 (t0) cc_final: 0.6548 (t0)
REVERT: A  163 GLU cc_start: 0.8152 (tp30) cc_final: 0.7932 (mm-30)
REVERT: A  165 LYS cc_start: 0.8675 (pttm) cc_final: 0.8470 (pttm)
REVERT: A  182 MET cc_start: 0.4204 (mmm) cc_final: 0.3794 (mmm)
REVERT: A  183 LYS cc_start: 0.8546 (tttt) cc_final: 0.8308 (ptpp)
REVERT: B   59 PHE cc_start: 0.7499 (t80) cc_final: 0.7259 (t80)
REVERT: B   66 GLU cc_start: 0.5957 (pp20) cc_final: 0.5700 (pm20)
REVERT: B  145 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6911 (mm-30)
REVERT: B  156 HIS cc_start: 0.6834 (p90) cc_final: 0.6409 (p-80)
REVERT: B  158 LYS cc_start: 0.8125 (tptp) cc_final: 0.7800 (tppt)
REVERT: C    2 LYS cc_start: 0.8073 (tptp) cc_final: 0.7797 (tppt)
REVERT: C   66 LYS cc_start: 0.7043 (tttt) cc_final: 0.6684 (ttpt)
REVERT: C   78 LEU cc_start: 0.7879 (mt) cc_final: 0.7620 (mt)
REVERT: C  187 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6168 (tm-30)
REVERT: C  230 MET cc_start: 0.0375 (mtp) cc_final: 0.0129 (ttm)
REVERT: E   54 LEU cc_start: 0.8528 (mm) cc_final: 0.8243 (mt)
REVERT: E   64 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7723 (mtpp)
REVERT: E   99 LYS cc_start: 0.8096 (tttt) cc_final: 0.7848 (tttt)
REVERT: E  123 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6460 (tm-30)
REVERT: E  288 GLN cc_start: 0.7795 (mt0) cc_final: 0.7049 (mp10)
REVERT: E  304 GLU cc_start: 0.7605 (pm20) cc_final: 0.7193 (pm20)
REVERT: E  338 GLU cc_start: 0.7048 (tp30) cc_final: 0.6454 (tp30)
REVERT: E  342 GLU cc_start: 0.7283 (tp30) cc_final: 0.6759 (tm-30)
REVERT: E  430 LEU cc_start: 0.8299 (tt) cc_final: 0.8052 (tt)
REVERT: E  583 MET cc_start: 0.8706 (mtp) cc_final: 0.8473 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 230
  average time/residue: 0.3244
  time to fit residues: 97.9799
Evaluate side-chains
  203 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 134 optimal weight:   30.0000
   chunk 105 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 113 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 136 optimal weight:    9.9990
   chunk 87 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 2 optimal weight:    3.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 284 ASN
** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.182224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.151448 restraints weight = 23205.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.155933 restraints weight = 14340.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.159107 restraints weight = 9885.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.4214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4217
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4217 r_free = 0.4217    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4217 r_free = 0.4217    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4217
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6312
moved from start:          0.4180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.070  12074  Z= 0.301
  Angle     :  0.800  10.693  16547  Z= 0.426
  Chirality :  0.050   0.230   1896
  Planarity :  0.005   0.051   1892
  Dihedral  : 19.605 164.337   2087
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 23.16
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 13.19 %
    Favored  : 86.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.20 (0.21), residues: 1319
  helix: -1.86 (0.27), residues: 307
  sheet: -1.16 (0.28), residues: 335
  loop : -2.81 (0.21), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP E 429 
 HIS   0.006   0.001   HIS B 156 
 PHE   0.035   0.003   PHE E 165 
 TYR   0.029   0.003   TYR E  56 
 ARG   0.008   0.001   ARG B 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06139 (  386)
  hydrogen bonds       : angle       6.93192 (  988)
  covalent geometry    : bond        0.00656 (12074)
  covalent geometry    : angle       0.80005 (16547)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 1.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.7186 (t0) cc_final: 0.6458 (t0)
REVERT: A  116 LYS cc_start: 0.8454 (tptp) cc_final: 0.8081 (mtpp)
REVERT: A  164 ASP cc_start: 0.7967 (t0) cc_final: 0.5876 (t0)
REVERT: A  165 LYS cc_start: 0.8820 (pttm) cc_final: 0.8527 (pttm)
REVERT: A  182 MET cc_start: 0.4778 (mmm) cc_final: 0.4209 (mmm)
REVERT: A  183 LYS cc_start: 0.8570 (tttt) cc_final: 0.8228 (tppt)
REVERT: A  244 TRP cc_start: 0.7037 (m100) cc_final: 0.6572 (m100)
REVERT: B   26 ASN cc_start: 0.8276 (t0) cc_final: 0.8066 (t0)
REVERT: B   59 PHE cc_start: 0.7438 (t80) cc_final: 0.7238 (t80)
REVERT: B  145 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7165 (mm-30)
REVERT: B  156 HIS cc_start: 0.6657 (p90) cc_final: 0.6400 (p-80)
REVERT: B  158 LYS cc_start: 0.8192 (tptp) cc_final: 0.7947 (tppt)
REVERT: B  199 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7189 (tm-30)
REVERT: B  243 ARG cc_start: 0.8288 (tpp-160) cc_final: 0.8041 (tpp80)
REVERT: C   66 LYS cc_start: 0.7439 (tttt) cc_final: 0.7005 (ttpt)
REVERT: C   78 LEU cc_start: 0.7924 (mt) cc_final: 0.7596 (mt)
REVERT: C  112 ARG cc_start: 0.7505 (ptm-80) cc_final: 0.6938 (ptm-80)
REVERT: C  115 GLU cc_start: 0.8382 (tp30) cc_final: 0.7754 (tp30)
REVERT: C  230 MET cc_start: 0.0821 (mtp) cc_final: 0.0594 (ttm)
REVERT: E   54 LEU cc_start: 0.8628 (mm) cc_final: 0.8385 (mt)
REVERT: E   63 GLU cc_start: 0.6897 (tt0) cc_final: 0.6650 (tt0)
REVERT: E   66 LEU cc_start: 0.7810 (mt) cc_final: 0.7505 (mt)
REVERT: E  123 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6972 (tm-30)
REVERT: E  180 LEU cc_start: 0.7746 (mt) cc_final: 0.7477 (mt)
REVERT: E  181 ASP cc_start: 0.7464 (m-30) cc_final: 0.6977 (t0)
REVERT: E  258 ASP cc_start: 0.7249 (p0) cc_final: 0.7016 (p0)
REVERT: E  304 GLU cc_start: 0.7810 (pm20) cc_final: 0.7450 (pm20)
REVERT: E  314 ILE cc_start: 0.7776 (mm) cc_final: 0.7545 (mm)
REVERT: E  338 GLU cc_start: 0.7459 (tp30) cc_final: 0.7205 (tp30)
REVERT: E  342 GLU cc_start: 0.7481 (tp30) cc_final: 0.6957 (tm-30)
REVERT: E  583 MET cc_start: 0.8704 (mtp) cc_final: 0.8482 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 232
  average time/residue: 0.3744
  time to fit residues: 115.5453
Evaluate side-chains
  200 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 118 optimal weight:    9.9990
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 114 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 111 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0770
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.8740

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

Flipped N/Q/H residues before XYZ refinement:
E 202 ASN
E 284 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.188678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.158746 restraints weight = 23526.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.163399 restraints weight = 14211.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.166665 restraints weight = 9649.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4316
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4316 r_free = 0.4316    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4316 r_free = 0.4316    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4316
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6145
moved from start:          0.4428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12074  Z= 0.155
  Angle     :  0.670   8.092  16547  Z= 0.353
  Chirality :  0.046   0.191   1896
  Planarity :  0.004   0.052   1892
  Dihedral  : 19.670 165.828   2087
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 15.98
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.54 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.00 (0.22), residues: 1319
  helix: -1.57 (0.28), residues: 303
  sheet: -1.12 (0.30), residues: 326
  loop : -2.68 (0.21), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E 431 
 HIS   0.002   0.001   HIS E 510 
 PHE   0.024   0.002   PHE B  27 
 TYR   0.023   0.002   TYR B 196 
 ARG   0.007   0.001   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04064 (  386)
  hydrogen bonds       : angle       6.31060 (  988)
  covalent geometry    : bond        0.00343 (12074)
  covalent geometry    : angle       0.67000 (16547)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 2.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LYS cc_start: 0.7886 (ptpp) cc_final: 0.7481 (ptpp)
REVERT: A   24 ASP cc_start: 0.7297 (t0) cc_final: 0.6930 (t0)
REVERT: A   29 ASN cc_start: 0.6973 (t0) cc_final: 0.6710 (m110)
REVERT: A  110 LYS cc_start: 0.8784 (tttt) cc_final: 0.8403 (ttmm)
REVERT: A  116 LYS cc_start: 0.8457 (tptp) cc_final: 0.8233 (tptp)
REVERT: A  164 ASP cc_start: 0.8008 (t0) cc_final: 0.6158 (t0)
REVERT: A  182 MET cc_start: 0.4431 (mmm) cc_final: 0.3940 (mmm)
REVERT: A  183 LYS cc_start: 0.8575 (tttt) cc_final: 0.8207 (tppt)
REVERT: A  210 LYS cc_start: 0.8800 (ptmt) cc_final: 0.8245 (ptpt)
REVERT: B   22 LEU cc_start: 0.8387 (mp) cc_final: 0.8139 (mt)
REVERT: B   26 ASN cc_start: 0.8101 (t0) cc_final: 0.7809 (t0)
REVERT: B   35 ARG cc_start: 0.7779 (ptp-110) cc_final: 0.7453 (ptp-110)
REVERT: B  145 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7066 (mm-30)
REVERT: B  156 HIS cc_start: 0.6808 (p90) cc_final: 0.6325 (p-80)
REVERT: B  158 LYS cc_start: 0.8160 (tptp) cc_final: 0.7836 (tppt)
REVERT: B  225 LYS cc_start: 0.6678 (tttt) cc_final: 0.6223 (tttm)
REVERT: C   78 LEU cc_start: 0.7970 (mt) cc_final: 0.7670 (mt)
REVERT: C   79 LYS cc_start: 0.7835 (pttt) cc_final: 0.7493 (pttp)
REVERT: C  112 ARG cc_start: 0.7223 (ptm-80) cc_final: 0.6832 (ptm-80)
REVERT: C  230 MET cc_start: 0.0701 (mtp) cc_final: 0.0424 (ttm)
REVERT: E   29 LEU cc_start: 0.7876 (tp) cc_final: 0.7474 (mm)
REVERT: E   54 LEU cc_start: 0.8581 (mm) cc_final: 0.8323 (mt)
REVERT: E   66 LEU cc_start: 0.7822 (mt) cc_final: 0.7514 (mt)
REVERT: E   99 LYS cc_start: 0.8224 (tttt) cc_final: 0.7955 (tttt)
REVERT: E  123 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6947 (tm-30)
REVERT: E  160 LYS cc_start: 0.7340 (mttp) cc_final: 0.7055 (pttm)
REVERT: E  180 LEU cc_start: 0.7721 (mt) cc_final: 0.7452 (mt)
REVERT: E  181 ASP cc_start: 0.7365 (m-30) cc_final: 0.6990 (t0)
REVERT: E  258 ASP cc_start: 0.7095 (p0) cc_final: 0.6702 (p0)
REVERT: E  288 GLN cc_start: 0.7755 (mt0) cc_final: 0.7054 (mp10)
REVERT: E  304 GLU cc_start: 0.7687 (pm20) cc_final: 0.7477 (pm20)
REVERT: E  338 GLU cc_start: 0.7294 (tp30) cc_final: 0.6980 (tp30)
REVERT: E  342 GLU cc_start: 0.7415 (tp30) cc_final: 0.6804 (tm-30)
REVERT: E  353 MET cc_start: 0.6705 (ptt) cc_final: 0.6466 (ptp)
REVERT: E  583 MET cc_start: 0.8707 (mtp) cc_final: 0.8496 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.4518
  time to fit residues: 140.5368
Evaluate side-chains
  192 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 2.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 70 optimal weight:    0.2980
   chunk 73 optimal weight:    3.9990
   chunk 129 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 122 optimal weight:    0.3980
   chunk 63 optimal weight:    0.0870
   chunk 65 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 115 optimal weight:    0.9980
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
** C 225 GLN ** 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 = 0.4601 r_free = 0.4601 target = 0.189929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.159807 restraints weight = 23548.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.164542 restraints weight = 14238.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.167884 restraints weight = 9639.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.4322
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4321 r_free = 0.4321    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4321 r_free = 0.4321    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6138
moved from start:          0.4648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12074  Z= 0.146
  Angle     :  0.666   8.775  16547  Z= 0.349
  Chirality :  0.046   0.209   1896
  Planarity :  0.004   0.053   1892
  Dihedral  : 19.552 165.848   2087
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 10.61 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.85 (0.22), residues: 1319
  helix: -1.41 (0.28), residues: 300
  sheet: -1.09 (0.29), residues: 331
  loop : -2.58 (0.22), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 244 
 HIS   0.002   0.001   HIS B 156 
 PHE   0.022   0.002   PHE A  12 
 TYR   0.017   0.001   TYR A 177 
 ARG   0.007   0.000   ARG E 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  386)
  hydrogen bonds       : angle       6.09110 (  988)
  covalent geometry    : bond        0.00327 (12074)
  covalent geometry    : angle       0.66556 (16547)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 1.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.7312 (t0) cc_final: 0.6763 (t0)
REVERT: A   86 LYS cc_start: 0.8249 (pttp) cc_final: 0.7265 (pttp)
REVERT: A  110 LYS cc_start: 0.8893 (tttt) cc_final: 0.8602 (ttmm)
REVERT: A  116 LYS cc_start: 0.8448 (tptp) cc_final: 0.8207 (tptp)
REVERT: A  123 GLU cc_start: 0.8444 (pm20) cc_final: 0.7988 (pm20)
REVERT: A  164 ASP cc_start: 0.7906 (t0) cc_final: 0.6209 (t0)
REVERT: A  182 MET cc_start: 0.4385 (mmm) cc_final: 0.3907 (mmm)
REVERT: A  183 LYS cc_start: 0.8539 (tttt) cc_final: 0.8175 (tppt)
REVERT: A  210 LYS cc_start: 0.8814 (ptmt) cc_final: 0.8265 (ptpt)
REVERT: A  229 MET cc_start: 0.4144 (ttm) cc_final: 0.3917 (ttm)
REVERT: A  244 TRP cc_start: 0.7451 (m100) cc_final: 0.7169 (m100)
REVERT: B   22 LEU cc_start: 0.8314 (mp) cc_final: 0.8109 (mt)
REVERT: B   26 ASN cc_start: 0.8001 (t0) cc_final: 0.7787 (t0)
REVERT: B  156 HIS cc_start: 0.6770 (p90) cc_final: 0.6294 (p-80)
REVERT: B  158 LYS cc_start: 0.8132 (tptp) cc_final: 0.7893 (tppt)
REVERT: C   78 LEU cc_start: 0.7986 (mt) cc_final: 0.7719 (mt)
REVERT: C   79 LYS cc_start: 0.7747 (pttt) cc_final: 0.7431 (pttp)
REVERT: C  112 ARG cc_start: 0.7285 (ptm-80) cc_final: 0.6886 (ptm-80)
REVERT: C  230 MET cc_start: 0.0442 (mtp) cc_final: 0.0187 (ttm)
REVERT: E   29 LEU cc_start: 0.7823 (tp) cc_final: 0.7453 (mm)
REVERT: E   54 LEU cc_start: 0.8553 (mm) cc_final: 0.8297 (mt)
REVERT: E  123 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6933 (tm-30)
REVERT: E  258 ASP cc_start: 0.7105 (p0) cc_final: 0.6663 (p0)
REVERT: E  288 GLN cc_start: 0.7714 (mt0) cc_final: 0.7342 (mt0)
REVERT: E  304 GLU cc_start: 0.7699 (pm20) cc_final: 0.7454 (pm20)
REVERT: E  338 GLU cc_start: 0.7178 (tp30) cc_final: 0.6892 (tp30)
REVERT: E  342 GLU cc_start: 0.7407 (tp30) cc_final: 0.6807 (tm-30)
REVERT: E  583 MET cc_start: 0.8648 (mtp) cc_final: 0.8421 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.4085
  time to fit residues: 124.9936
Evaluate side-chains
  195 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 110 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0670
   chunk 125 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 104 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 78 optimal weight:    4.9990
   chunk 67 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.6520

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

Flipped N/Q/H residues before XYZ refinement:
** C 225 GLN ** 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 = 0.4609 r_free = 0.4609 target = 0.190846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.160815 restraints weight = 23418.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.165636 restraints weight = 14073.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.168933 restraints weight = 9494.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4337
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4337 r_free = 0.4337    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4337 r_free = 0.4337    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4337
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6105
moved from start:          0.4832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12074  Z= 0.138
  Angle     :  0.660   9.056  16547  Z= 0.345
  Chirality :  0.045   0.210   1896
  Planarity :  0.004   0.053   1892
  Dihedral  : 19.484 166.369   2087
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.93 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.82 (0.22), residues: 1319
  helix: -1.26 (0.29), residues: 301
  sheet: -1.16 (0.28), residues: 341
  loop : -2.58 (0.22), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  39 
 PHE   0.026   0.002   PHE B  56 
 TYR   0.017   0.001   TYR E 422 
 ARG   0.004   0.000   ARG B 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  386)
  hydrogen bonds       : angle       5.86207 (  988)
  covalent geometry    : bond        0.00310 (12074)
  covalent geometry    : angle       0.65983 (16547)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 1.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.7275 (t0) cc_final: 0.6918 (t0)
REVERT: A   62 ILE cc_start: 0.8537 (mp) cc_final: 0.8328 (pt)
REVERT: A   91 LEU cc_start: 0.7733 (tp) cc_final: 0.6758 (pt)
REVERT: A  164 ASP cc_start: 0.7923 (t0) cc_final: 0.6119 (t0)
REVERT: A  165 LYS cc_start: 0.9045 (ptpp) cc_final: 0.8683 (pttm)
REVERT: A  182 MET cc_start: 0.4128 (mmm) cc_final: 0.3721 (mmm)
REVERT: A  183 LYS cc_start: 0.8564 (tttt) cc_final: 0.8298 (tppt)
REVERT: A  210 LYS cc_start: 0.8820 (ptmt) cc_final: 0.8282 (ptpt)
REVERT: A  229 MET cc_start: 0.4847 (ttm) cc_final: 0.4473 (ttm)
REVERT: A  244 TRP cc_start: 0.7260 (m100) cc_final: 0.6838 (m100)
REVERT: B   22 LEU cc_start: 0.8431 (mp) cc_final: 0.8120 (mt)
REVERT: B   26 ASN cc_start: 0.7967 (t0) cc_final: 0.7726 (t0)
REVERT: B   35 ARG cc_start: 0.8022 (ptp-110) cc_final: 0.7726 (ptp-110)
REVERT: B   68 ILE cc_start: 0.8474 (mp) cc_final: 0.7780 (mm)
REVERT: B  145 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7070 (mm-30)
REVERT: B  158 LYS cc_start: 0.8123 (tptp) cc_final: 0.7842 (tppt)
REVERT: C  230 MET cc_start: 0.0300 (mtp) cc_final: 0.0053 (ttm)
REVERT: E   29 LEU cc_start: 0.7876 (tp) cc_final: 0.7476 (mm)
REVERT: E   66 LEU cc_start: 0.7426 (mm) cc_final: 0.7095 (mm)
REVERT: E   99 LYS cc_start: 0.8079 (tttt) cc_final: 0.7783 (tttt)
REVERT: E  123 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6808 (tm-30)
REVERT: E  258 ASP cc_start: 0.7200 (p0) cc_final: 0.6604 (p0)
REVERT: E  259 TYR cc_start: 0.6841 (m-80) cc_final: 0.6450 (m-80)
REVERT: E  288 GLN cc_start: 0.7703 (mt0) cc_final: 0.7318 (mt0)
REVERT: E  304 GLU cc_start: 0.7911 (pm20) cc_final: 0.7512 (pm20)
REVERT: E  308 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7035 (tm-30)
REVERT: E  338 GLU cc_start: 0.7231 (tp30) cc_final: 0.6768 (tp30)
REVERT: E  342 GLU cc_start: 0.7436 (tp30) cc_final: 0.6807 (tm-30)
REVERT: E  353 MET cc_start: 0.6557 (ptp) cc_final: 0.6223 (ttp)
REVERT: E  583 MET cc_start: 0.8663 (mtp) cc_final: 0.8426 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.3686
  time to fit residues: 109.7918
Evaluate side-chains
  184 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 125 optimal weight:    0.5980
   chunk 126 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0870
   chunk 110 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 108 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   overall best weight:    1.0960

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

Flipped N/Q/H residues before XYZ refinement:
E 386 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.188285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.158317 restraints weight = 23389.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.162935 restraints weight = 14294.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.166178 restraints weight = 9730.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.4311
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4310
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4310 r_free = 0.4310    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4310 r_free = 0.4310    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4310
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6159
moved from start:          0.4895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12074  Z= 0.165
  Angle     :  0.688   8.626  16547  Z= 0.360
  Chirality :  0.046   0.190   1896
  Planarity :  0.004   0.053   1892
  Dihedral  : 19.444 166.246   2087
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 16.15
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 11.37 %
    Favored  : 88.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.80 (0.22), residues: 1319
  helix: -1.21 (0.29), residues: 295
  sheet: -1.13 (0.28), residues: 351
  loop : -2.62 (0.22), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 244 
 HIS   0.003   0.001   HIS A  39 
 PHE   0.032   0.002   PHE A  12 
 TYR   0.015   0.002   TYR A 177 
 ARG   0.005   0.000   ARG E 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04070 (  386)
  hydrogen bonds       : angle       6.01680 (  988)
  covalent geometry    : bond        0.00368 (12074)
  covalent geometry    : angle       0.68761 (16547)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.7709 (t80) cc_final: 0.7467 (t80)
REVERT: A   24 ASP cc_start: 0.7309 (t0) cc_final: 0.6913 (t0)
REVERT: A   47 MET cc_start: 0.4370 (ptt) cc_final: 0.4088 (ppp)
REVERT: A   49 ILE cc_start: 0.7107 (mt) cc_final: 0.6151 (mt)
REVERT: A   91 LEU cc_start: 0.7678 (tp) cc_final: 0.6688 (pt)
REVERT: A  164 ASP cc_start: 0.7929 (t0) cc_final: 0.5919 (t0)
REVERT: A  165 LYS cc_start: 0.8901 (ptpp) cc_final: 0.8589 (pttm)
REVERT: A  182 MET cc_start: 0.3970 (mmm) cc_final: 0.3590 (mmm)
REVERT: A  183 LYS cc_start: 0.8603 (tttt) cc_final: 0.8299 (tppt)
REVERT: A  210 LYS cc_start: 0.8827 (ptmt) cc_final: 0.8345 (ptpt)
REVERT: A  229 MET cc_start: 0.4428 (ttm) cc_final: 0.4193 (ttm)
REVERT: A  244 TRP cc_start: 0.7272 (m100) cc_final: 0.6636 (m100)
REVERT: B   26 ASN cc_start: 0.7898 (t0) cc_final: 0.7568 (t0)
REVERT: B   35 ARG cc_start: 0.7851 (ptp-110) cc_final: 0.7616 (ptp-110)
REVERT: B   59 PHE cc_start: 0.7568 (t80) cc_final: 0.7284 (t80)
REVERT: B  156 HIS cc_start: 0.6668 (p-80) cc_final: 0.6355 (p-80)
REVERT: B  158 LYS cc_start: 0.8138 (tptp) cc_final: 0.7895 (tppt)
REVERT: B  243 ARG cc_start: 0.7800 (tpp-160) cc_final: 0.7568 (tpp80)
REVERT: C  112 ARG cc_start: 0.7338 (ptm-80) cc_final: 0.6896 (ptm-80)
REVERT: C  230 MET cc_start: 0.0469 (mtp) cc_final: 0.0198 (ttm)
REVERT: E   29 LEU cc_start: 0.7826 (tp) cc_final: 0.7548 (mt)
REVERT: E   66 LEU cc_start: 0.7644 (mm) cc_final: 0.7355 (mm)
REVERT: E   99 LYS cc_start: 0.8111 (tttt) cc_final: 0.7792 (tttt)
REVERT: E  123 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7134 (tm-30)
REVERT: E  160 LYS cc_start: 0.7201 (ptpp) cc_final: 0.6865 (mptt)
REVERT: E  226 LYS cc_start: 0.5673 (mtpt) cc_final: 0.5406 (mtpp)
REVERT: E  228 GLN cc_start: 0.5731 (pm20) cc_final: 0.5509 (pm20)
REVERT: E  258 ASP cc_start: 0.7285 (p0) cc_final: 0.6680 (p0)
REVERT: E  288 GLN cc_start: 0.7683 (mt0) cc_final: 0.7232 (mp10)
REVERT: E  304 GLU cc_start: 0.7903 (pm20) cc_final: 0.7579 (pm20)
REVERT: E  308 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7110 (tm-30)
REVERT: E  338 GLU cc_start: 0.7224 (tp30) cc_final: 0.6743 (tp30)
REVERT: E  342 GLU cc_start: 0.7472 (tp30) cc_final: 0.6850 (tm-30)
REVERT: E  353 MET cc_start: 0.6386 (ptp) cc_final: 0.5967 (ttp)
REVERT: E  583 MET cc_start: 0.8677 (mtp) cc_final: 0.8417 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.4191
  time to fit residues: 121.1212
Evaluate side-chains
  189 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 118 optimal weight:    9.9990
   chunk 96 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 80 optimal weight:    0.0370
   chunk 4 optimal weight:    0.8980
   chunk 130 optimal weight:    0.0050
   chunk 86 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 108 optimal weight:    0.1980
   overall best weight:    0.4072

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

Flipped N/Q/H residues before XYZ refinement:
B 181 ASN
** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 386 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.191655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.163707 restraints weight = 23377.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.168259 restraints weight = 14302.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.171393 restraints weight = 9728.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.4388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4398
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4398 r_free = 0.4398    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4398 r_free = 0.4398    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4398
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6051
moved from start:          0.5092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12074  Z= 0.127
  Angle     :  0.662   9.453  16547  Z= 0.344
  Chirality :  0.045   0.189   1896
  Planarity :  0.004   0.054   1892
  Dihedral  : 19.452 166.908   2087
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.25 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.64 (0.22), residues: 1319
  helix: -1.04 (0.30), residues: 294
  sheet: -0.92 (0.29), residues: 329
  loop : -2.55 (0.22), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP E 431 
 HIS   0.002   0.001   HIS A  39 
 PHE   0.030   0.002   PHE A  12 
 TYR   0.018   0.001   TYR E 422 
 ARG   0.006   0.000   ARG B 227 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03386 (  386)
  hydrogen bonds       : angle       5.78955 (  988)
  covalent geometry    : bond        0.00284 (12074)
  covalent geometry    : angle       0.66165 (16547)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 1.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.7229 (t0) cc_final: 0.6862 (t0)
REVERT: A   47 MET cc_start: 0.4447 (ptt) cc_final: 0.4240 (ppp)
REVERT: A   49 ILE cc_start: 0.7037 (mt) cc_final: 0.6147 (mt)
REVERT: A   55 ASP cc_start: 0.4995 (p0) cc_final: 0.4496 (p0)
REVERT: A  164 ASP cc_start: 0.7884 (t0) cc_final: 0.5748 (t0)
REVERT: A  182 MET cc_start: 0.3965 (mmm) cc_final: 0.3568 (mmm)
REVERT: A  183 LYS cc_start: 0.8609 (tttt) cc_final: 0.8237 (tppt)
REVERT: A  210 LYS cc_start: 0.8800 (ptmt) cc_final: 0.8266 (ptpt)
REVERT: A  229 MET cc_start: 0.4338 (ttm) cc_final: 0.4136 (ttm)
REVERT: A  244 TRP cc_start: 0.6854 (m100) cc_final: 0.6282 (m100)
REVERT: B   26 ASN cc_start: 0.7830 (t0) cc_final: 0.7553 (t0)
REVERT: B   59 PHE cc_start: 0.7618 (t80) cc_final: 0.7328 (t80)
REVERT: B  156 HIS cc_start: 0.6691 (p-80) cc_final: 0.6362 (p-80)
REVERT: B  158 LYS cc_start: 0.8124 (tptp) cc_final: 0.7866 (tppt)
REVERT: B  243 ARG cc_start: 0.7713 (tpp-160) cc_final: 0.7505 (tpp80)
REVERT: C   50 ASN cc_start: 0.7498 (t0) cc_final: 0.6968 (t0)
REVERT: C  112 ARG cc_start: 0.7122 (ptm-80) cc_final: 0.6779 (ptm-80)
REVERT: C  230 MET cc_start: 0.0535 (mtp) cc_final: 0.0235 (ttm)
REVERT: E   29 LEU cc_start: 0.8169 (tp) cc_final: 0.7788 (mt)
REVERT: E   54 LEU cc_start: 0.8567 (mm) cc_final: 0.8328 (mt)
REVERT: E   66 LEU cc_start: 0.7442 (mm) cc_final: 0.7137 (mm)
REVERT: E   99 LYS cc_start: 0.8083 (tttt) cc_final: 0.7695 (tttt)
REVERT: E  123 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6664 (tm-30)
REVERT: E  127 THR cc_start: 0.8094 (t) cc_final: 0.7849 (t)
REVERT: E  233 ILE cc_start: 0.7026 (mt) cc_final: 0.6749 (tt)
REVERT: E  258 ASP cc_start: 0.7348 (p0) cc_final: 0.6717 (p0)
REVERT: E  288 GLN cc_start: 0.7602 (mt0) cc_final: 0.7229 (mt0)
REVERT: E  304 GLU cc_start: 0.7975 (pm20) cc_final: 0.7615 (pm20)
REVERT: E  338 GLU cc_start: 0.7022 (tp30) cc_final: 0.6572 (tp30)
REVERT: E  342 GLU cc_start: 0.7393 (tp30) cc_final: 0.6743 (tm-30)
REVERT: E  353 MET cc_start: 0.6503 (ptp) cc_final: 0.6206 (ttp)
REVERT: E  583 MET cc_start: 0.8699 (mtp) cc_final: 0.8437 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.4743
  time to fit residues: 134.6198
Evaluate side-chains
  176 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 2.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 131 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0060
   chunk 95 optimal weight:    0.3980
   chunk 69 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 98 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    1.2800

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

Flipped N/Q/H residues before XYZ refinement:
E 386 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.187946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.159370 restraints weight = 23632.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.163792 restraints weight = 14502.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.166860 restraints weight = 9930.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.4328
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4334
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4334 r_free = 0.4334    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4334 r_free = 0.4334    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4334
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6167
moved from start:          0.5125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12074  Z= 0.178
  Angle     :  0.701   9.550  16547  Z= 0.366
  Chirality :  0.047   0.230   1896
  Planarity :  0.004   0.053   1892
  Dihedral  : 19.378 166.121   2087
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 11.75 %
    Favored  : 88.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.65 (0.22), residues: 1319
  helix: -1.08 (0.30), residues: 295
  sheet: -0.90 (0.29), residues: 336
  loop : -2.58 (0.22), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP E 431 
 HIS   0.004   0.001   HIS A  39 
 PHE   0.035   0.002   PHE A  12 
 TYR   0.017   0.002   TYR E 422 
 ARG   0.004   0.000   ARG E 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04174 (  386)
  hydrogen bonds       : angle       5.97874 (  988)
  covalent geometry    : bond        0.00397 (12074)
  covalent geometry    : angle       0.70052 (16547)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4956.46 seconds
wall clock time: 92 minutes 15.73 seconds (5535.73 seconds total)