Starting phenix.real_space_refine
on Wed Mar  4 07:11:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rpx_24625/03_2026/7rpx_24625.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rpx_24625/03_2026/7rpx_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_24625/03_2026/7rpx_24625.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rpx_24625/03_2026/7rpx_24625.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rpx_24625/03_2026/7rpx_24625.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rpx_24625/03_2026/7rpx_24625.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.53, per 1000 atoms: 0.22
  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: 0.77
  Conformation dependent library (CDL) restraints added in 412.1 milliseconds
  

  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: 1.37
  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: 1.68

  Time building geometry restraints manager: 1.09 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:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.830
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.940
-------------------------------------------------------------------------------
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 : 21.81
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.002   0.000   ARG E 140 
 TYR   0.022   0.001   TYR C 200 
 PHE   0.014   0.001   PHE B 101 
 TRP   0.013   0.001   TRP E 431 
 HIS   0.002   0.001   HIS B 156 

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

*********************** 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  : 0.295 
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: symmetry clash
REVERT: A   12 PHE cc_start: 0.7372 (t80) cc_final: 0.7114 (t80)
REVERT: A   24 ASP cc_start: 0.6700 (t0) cc_final: 0.6025 (t0)
REVERT: A   26 ILE cc_start: 0.8107 (pt) cc_final: 0.7892 (pt)
REVERT: A   29 ASN cc_start: 0.6231 (m-40) cc_final: 0.5648 (m110)
REVERT: A   30 PHE cc_start: 0.8159 (m-80) cc_final: 0.7948 (m-80)
REVERT: A   69 LYS cc_start: 0.7697 (tppt) cc_final: 0.7478 (tppt)
REVERT: A   86 LYS cc_start: 0.8023 (pttp) cc_final: 0.7302 (pptt)
REVERT: A  164 ASP cc_start: 0.7677 (t0) cc_final: 0.5805 (t0)
REVERT: A  182 MET cc_start: 0.4462 (mmm) cc_final: 0.4133 (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: 0.8308 (ptpt)
REVERT: A  213 ARG cc_start: 0.5305 (OUTLIER) cc_final: 0.4581 (mpp80)
REVERT: A  232 ASP cc_start: 0.6464 (t0) cc_final: 0.6008 (t0)
REVERT: A  244 TRP cc_start: 0.7138 (m100) cc_final: 0.6772 (m100)
REVERT: B   11 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.6350 (t80)
REVERT: B   16 ARG cc_start: 0.7724 (mtm180) cc_final: 0.7433 (ttm-80)
REVERT: B   55 TYR cc_start: 0.4681 (OUTLIER) cc_final: 0.1758 (t80)
REVERT: B   68 ILE cc_start: 0.8603 (mt) cc_final: 0.8102 (mm)
REVERT: B  156 HIS cc_start: 0.6874 (p90) cc_final: 0.6504 (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: 0.4308 (t0)
REVERT: C   83 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7832 (mpp80)
REVERT: C  128 PHE cc_start: 0.6685 (m-80) cc_final: 0.4540 (m-10)
REVERT: C  165 LYS cc_start: 0.6958 (pttp) cc_final: 0.6601 (pttp)
REVERT: E  145 ARG cc_start: 0.5175 (OUTLIER) cc_final: 0.4534 (ttm-80)
REVERT: E  162 LEU cc_start: 0.7773 (mt) cc_final: 0.7260 (mt)
REVERT: E  213 ILE cc_start: 0.8145 (mt) cc_final: 0.7722 (mt)
REVERT: E  303 LYS cc_start: 0.8829 (mptp) cc_final: 0.8519 (mmtm)
REVERT: E  454 PHE cc_start: 0.5176 (m-80) cc_final: 0.3306 (m-80)
REVERT: E  517 MET cc_start: 0.5501 (ttm) cc_final: 0.5163 (ttm)
REVERT: E  583 MET cc_start: 0.8854 (mtp) cc_final: 0.8507 (mtp)
  outliers start: 10
  outliers final: 2
  residues processed: 302
  average time/residue: 0.1405
  time to fit residues: 55.5040
Evaluate side-chains
  222 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 216
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    0.4980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C  43 HIS
** C  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 288 GLN
E 346 ASN
E 386 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.188993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.159994 restraints weight = 23822.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.164604 restraints weight = 14616.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.167907 restraints weight = 10011.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.170247 restraints weight = 7414.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.172024 restraints weight = 5856.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.4390
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4389 r_free = 0.4389    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4387 r_free = 0.4387    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5978
moved from start:          0.2922

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= 0.163
  Angle     :  0.676   9.519  16547  Z= 0.361
  Chirality :  0.048   0.222   1896
  Planarity :  0.005   0.053   1892
  Dihedral  : 19.387 160.170   2087
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.93 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.03 %
    Favored  : 95.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.22), residues: 1319
  helix: -1.20 (0.29), residues: 307
  sheet: -0.85 (0.29), residues: 337
  loop : -2.58 (0.22), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 227 
 TYR   0.025   0.002   TYR B  13 
 PHE   0.028   0.002   PHE E 400 
 TRP   0.017   0.003   TRP E 431 
 HIS   0.002   0.001   HIS E 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (12074)
  covalent geometry    : angle       0.67580 (16547)
  hydrogen bonds       : bond        0.05116 (  386)
  hydrogen bonds       : angle       6.98062 (  988)

*********************** 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
  248 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 247
  time to evaluate  : 0.354 
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: 0.6689 (t0) cc_final: 0.5956 (t0)
REVERT: A  164 ASP cc_start: 0.7671 (t0) cc_final: 0.6172 (t0)
REVERT: A  165 LYS cc_start: 0.8648 (pttm) cc_final: 0.8000 (pttm)
REVERT: A  183 LYS cc_start: 0.9115 (tttt) cc_final: 0.8753 (mmtm)
REVERT: A  184 ASP cc_start: 0.7618 (t0) cc_final: 0.7179 (t0)
REVERT: A  185 LYS cc_start: 0.8131 (mmtm) cc_final: 0.7788 (mmtm)
REVERT: A  210 LYS cc_start: 0.8772 (ptmt) cc_final: 0.8027 (ptpp)
REVERT: A  244 TRP cc_start: 0.7084 (m100) cc_final: 0.6678 (m100)
REVERT: B   16 ARG cc_start: 0.7789 (mtm180) cc_final: 0.7559 (ttm-80)
REVERT: B   59 PHE cc_start: 0.7531 (t80) cc_final: 0.7288 (t80)
REVERT: B  145 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6835 (mm-30)
REVERT: B  156 HIS cc_start: 0.6931 (p90) cc_final: 0.6472 (p-80)
REVERT: B  206 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8183 (ttmm)
REVERT: C    2 LYS cc_start: 0.8104 (tptp) cc_final: 0.7889 (tppt)
REVERT: C   78 LEU cc_start: 0.7828 (mt) cc_final: 0.7577 (mt)
REVERT: C  115 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7635 (tm-30)
REVERT: C  165 LYS cc_start: 0.5270 (pttp) cc_final: 0.5047 (ptpp)
REVERT: C  230 MET cc_start: 0.0421 (mtp) cc_final: 0.0207 (mtp)
REVERT: E   99 LYS cc_start: 0.8102 (tttt) cc_final: 0.7802 (tttt)
REVERT: E  123 GLU cc_start: 0.6410 (tm-30) cc_final: 0.5910 (tm-30)
REVERT: E  160 LYS cc_start: 0.7481 (mttt) cc_final: 0.7028 (ptpp)
REVERT: E  180 LEU cc_start: 0.7538 (mt) cc_final: 0.7310 (mt)
REVERT: E  213 ILE cc_start: 0.8103 (mt) cc_final: 0.7764 (mt)
REVERT: E  264 GLU cc_start: 0.5645 (tm-30) cc_final: 0.5440 (tp30)
REVERT: E  304 GLU cc_start: 0.7478 (pm20) cc_final: 0.7163 (pm20)
REVERT: E  338 GLU cc_start: 0.7070 (tp30) cc_final: 0.6840 (tp30)
REVERT: E  583 MET cc_start: 0.8750 (mtp) cc_final: 0.8473 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 248
  average time/residue: 0.1412
  time to fit residues: 46.0532
Evaluate side-chains
  211 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 58 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.188040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.159153 restraints weight = 23889.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.163864 restraints weight = 14494.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.167193 restraints weight = 9834.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 65)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.169629 restraints weight = 7223.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.171297 restraints weight = 5669.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.4390
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4390
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4390 r_free = 0.4390    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4390 r_free = 0.4390    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.4390
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6009
moved from start:          0.3519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12074  Z= 0.155
  Angle     :  0.648   9.423  16547  Z= 0.345
  Chirality :  0.046   0.202   1896
  Planarity :  0.004   0.053   1892
  Dihedral  : 19.225 162.076   2087
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.01 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.17 %
    Favored  : 96.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.68 (0.22), residues: 1319
  helix: -1.07 (0.29), residues: 302
  sheet: -0.91 (0.29), residues: 333
  loop : -2.64 (0.22), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 112 
 TYR   0.020   0.002   TYR C 200 
 PHE   0.022   0.002   PHE B  27 
 TRP   0.016   0.003   TRP A 244 
 HIS   0.002   0.001   HIS E 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12074)
  covalent geometry    : angle       0.64844 (16547)
  hydrogen bonds       : bond        0.04391 (  386)
  hydrogen bonds       : angle       6.54585 (  988)

*********************** 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
  237 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 234
  time to evaluate  : 0.297 
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: 0.6955 (t0) cc_final: 0.6191 (t0)
REVERT: A   78 ILE cc_start: 0.8639 (mm) cc_final: 0.8138 (tp)
REVERT: A  165 LYS cc_start: 0.8607 (pttm) cc_final: 0.8292 (pttm)
REVERT: A  183 LYS cc_start: 0.8629 (tttt) cc_final: 0.8426 (ptpp)
REVERT: B    1 MET cc_start: 0.4948 (ttm) cc_final: 0.4675 (tpp)
REVERT: B   28 ILE cc_start: 0.5632 (OUTLIER) cc_final: 0.5302 (mp)
REVERT: B   59 PHE cc_start: 0.7516 (t80) cc_final: 0.7187 (t80)
REVERT: B   67 ILE cc_start: 0.8631 (mp) cc_final: 0.8426 (mm)
REVERT: B   68 ILE cc_start: 0.8197 (mp) cc_final: 0.7880 (mp)
REVERT: B  145 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6684 (mm-30)
REVERT: B  156 HIS cc_start: 0.6775 (p90) cc_final: 0.6335 (p-80)
REVERT: B  158 LYS cc_start: 0.8136 (tptp) cc_final: 0.7845 (tppt)
REVERT: B  206 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8119 (ttmm)
REVERT: B  218 PHE cc_start: 0.8270 (t80) cc_final: 0.7164 (t80)
REVERT: C   78 LEU cc_start: 0.7896 (mt) cc_final: 0.7597 (mt)
REVERT: C  112 ARG cc_start: 0.7426 (ptm-80) cc_final: 0.6840 (ptm-80)
REVERT: C  187 GLU cc_start: 0.6118 (tm-30) cc_final: 0.5572 (tm-30)
REVERT: C  230 MET cc_start: 0.0233 (mtp) cc_final: -0.0107 (ttm)
REVERT: E   99 LYS cc_start: 0.8110 (tttt) cc_final: 0.7851 (tttt)
REVERT: E  123 GLU cc_start: 0.6610 (tm-30) cc_final: 0.6279 (tm-30)
REVERT: E  166 VAL cc_start: 0.8986 (t) cc_final: 0.8710 (p)
REVERT: E  180 LEU cc_start: 0.7643 (mt) cc_final: 0.7442 (mt)
REVERT: E  258 ASP cc_start: 0.7145 (p0) cc_final: 0.6791 (p0)
REVERT: E  264 GLU cc_start: 0.5761 (tm-30) cc_final: 0.5483 (tp30)
REVERT: E  304 GLU cc_start: 0.7532 (pm20) cc_final: 0.7152 (pm20)
REVERT: E  338 GLU cc_start: 0.6959 (tp30) cc_final: 0.6400 (tp30)
REVERT: E  342 GLU cc_start: 0.7602 (tp30) cc_final: 0.7268 (tp30)
REVERT: E  583 MET cc_start: 0.8725 (mtp) cc_final: 0.8460 (mtp)
  outliers start: 3
  outliers final: 0
  residues processed: 237
  average time/residue: 0.1388
  time to fit residues: 43.2963
Evaluate side-chains
  203 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 202
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 123 optimal weight:   20.0000
   chunk 122 optimal weight:    0.9990
   chunk 101 optimal weight:    0.0570
   chunk 133 optimal weight:   30.0000
   chunk 32 optimal weight:    0.4980
   chunk 58 optimal weight:    0.7980
   chunk 117 optimal weight:    0.0170
   chunk 96 optimal weight:    0.0770
   chunk 72 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.2894

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.193161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.164540 restraints weight = 23887.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.169391 restraints weight = 14447.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.172900 restraints weight = 9693.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.175417 restraints weight = 7047.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.177240 restraints weight = 5473.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.4435
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4435
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4435 r_free = 0.4435    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4435 r_free = 0.4435    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.4435
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5905
moved from start:          0.4058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12074  Z= 0.127
  Angle     :  0.632   9.563  16547  Z= 0.331
  Chirality :  0.044   0.281   1896
  Planarity :  0.004   0.055   1892
  Dihedral  : 19.244 163.796   2087
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.93 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.00 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.22), residues: 1319
  helix: -0.82 (0.30), residues: 295
  sheet: -0.78 (0.30), residues: 306
  loop : -2.52 (0.21), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 227 
 TYR   0.019   0.002   TYR C  73 
 PHE   0.025   0.002   PHE B  27 
 TRP   0.016   0.002   TRP E 431 
 HIS   0.002   0.000   HIS E 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12074)
  covalent geometry    : angle       0.63161 (16547)
  hydrogen bonds       : bond        0.03613 (  386)
  hydrogen bonds       : angle       5.99007 (  988)

*********************** 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  : 0.441 
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: A   24 ASP cc_start: 0.7165 (t0) cc_final: 0.6637 (t0)
REVERT: A   78 ILE cc_start: 0.8622 (mm) cc_final: 0.8268 (tp)
REVERT: A  165 LYS cc_start: 0.8649 (pttm) cc_final: 0.8400 (pttm)
REVERT: A  183 LYS cc_start: 0.8547 (tttt) cc_final: 0.8322 (ptpp)
REVERT: A  244 TRP cc_start: 0.6674 (m100) cc_final: 0.6281 (m100)
REVERT: B   16 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7624 (ttm-80)
REVERT: B   26 ASN cc_start: 0.8049 (t0) cc_final: 0.7813 (t0)
REVERT: B   59 PHE cc_start: 0.7504 (t80) cc_final: 0.7225 (t80)
REVERT: B  145 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6651 (mm-30)
REVERT: B  156 HIS cc_start: 0.6683 (p90) cc_final: 0.6252 (p-80)
REVERT: B  158 LYS cc_start: 0.8105 (tptp) cc_final: 0.7806 (tppt)
REVERT: B  206 LYS cc_start: 0.8381 (ttmt) cc_final: 0.8139 (ttmm)
REVERT: B  214 MET cc_start: 0.7114 (ttt) cc_final: 0.6849 (ttt)
REVERT: B  218 PHE cc_start: 0.8282 (t80) cc_final: 0.6721 (t80)
REVERT: B  225 LYS cc_start: 0.6607 (tttm) cc_final: 0.6043 (tttm)
REVERT: C   78 LEU cc_start: 0.7833 (mt) cc_final: 0.7487 (mt)
REVERT: C   79 LYS cc_start: 0.7701 (pttt) cc_final: 0.7415 (pttm)
REVERT: C  187 GLU cc_start: 0.6688 (tm-30) cc_final: 0.6043 (tm-30)
REVERT: C  230 MET cc_start: 0.0129 (mtp) cc_final: -0.0164 (ttm)
REVERT: E   99 LYS cc_start: 0.8026 (tttt) cc_final: 0.7809 (tttt)
REVERT: E  123 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6865 (tm-30)
REVERT: E  288 GLN cc_start: 0.7745 (mt0) cc_final: 0.6949 (mp10)
REVERT: E  295 TYR cc_start: 0.7307 (m-10) cc_final: 0.7066 (m-80)
REVERT: E  304 GLU cc_start: 0.7570 (pm20) cc_final: 0.7207 (pm20)
REVERT: E  338 GLU cc_start: 0.6922 (tp30) cc_final: 0.6384 (tp30)
REVERT: E  342 GLU cc_start: 0.7554 (tp30) cc_final: 0.7142 (tp30)
REVERT: E  343 TYR cc_start: 0.6916 (m-80) cc_final: 0.6673 (m-10)
REVERT: E  412 MET cc_start: 0.4045 (mmp) cc_final: 0.3598 (mmp)
REVERT: E  414 LYS cc_start: 0.7480 (mmmt) cc_final: 0.7115 (mmmt)
REVERT: E  583 MET cc_start: 0.8722 (mtp) cc_final: 0.8461 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1400
  time to fit residues: 42.8596
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  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.4569 r_free = 0.4569 target = 0.186897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.156634 restraints weight = 23439.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.161249 restraints weight = 14327.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.164443 restraints weight = 9784.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.166766 restraints weight = 7294.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 62)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.168527 restraints weight = 5806.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.4337
-------------------------------------------------------------------------------
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:        5 |
|-----------------------------------------------------------------------------|
|-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:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4339
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6113
moved from start:          0.4103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12074  Z= 0.217
  Angle     :  0.707   9.556  16547  Z= 0.372
  Chirality :  0.047   0.305   1896
  Planarity :  0.004   0.052   1892
  Dihedral  : 19.263 163.406   2087
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 19.01
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 11.30 %
    Favored  : 88.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.22), residues: 1319
  helix: -1.38 (0.27), residues: 305
  sheet: -0.98 (0.28), residues: 344
  loop : -2.69 (0.22), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 227 
 TYR   0.025   0.002   TYR A   6 
 PHE   0.023   0.003   PHE B  27 
 TRP   0.015   0.002   TRP E 429 
 HIS   0.004   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (12074)
  covalent geometry    : angle       0.70720 (16547)
  hydrogen bonds       : bond        0.04836 (  386)
  hydrogen bonds       : angle       6.22839 (  988)

*********************** 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
  234 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.295 
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   24 ASP cc_start: 0.7253 (t0) cc_final: 0.6677 (t0)
REVERT: A   49 ILE cc_start: 0.7295 (mt) cc_final: 0.6732 (mt)
REVERT: A   78 ILE cc_start: 0.8703 (mm) cc_final: 0.8408 (tp)
REVERT: A  124 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7304 (tm-30)
REVERT: A  125 LEU cc_start: 0.7580 (pp) cc_final: 0.7332 (pp)
REVERT: A  164 ASP cc_start: 0.7755 (t70) cc_final: 0.6011 (t0)
REVERT: A  165 LYS cc_start: 0.8725 (pttm) cc_final: 0.8467 (pttm)
REVERT: A  183 LYS cc_start: 0.8508 (tttt) cc_final: 0.8215 (tppt)
REVERT: A  210 LYS cc_start: 0.8760 (ptmt) cc_final: 0.7961 (ptpp)
REVERT: A  244 TRP cc_start: 0.7024 (m100) cc_final: 0.6320 (m100)
REVERT: B   67 ILE cc_start: 0.8930 (mp) cc_final: 0.8615 (mp)
REVERT: B   68 ILE cc_start: 0.8639 (mp) cc_final: 0.7983 (mm)
REVERT: B  145 GLU cc_start: 0.7244 (mm-30) cc_final: 0.7027 (mm-30)
REVERT: B  156 HIS cc_start: 0.6734 (p90) cc_final: 0.6305 (p-80)
REVERT: B  158 LYS cc_start: 0.8140 (tptp) cc_final: 0.7905 (tppt)
REVERT: B  243 ARG cc_start: 0.8225 (tpp-160) cc_final: 0.7992 (tpp80)
REVERT: C    1 MET cc_start: 0.6571 (tmm) cc_final: 0.6330 (tmm)
REVERT: C   78 LEU cc_start: 0.7974 (mt) cc_final: 0.7648 (mt)
REVERT: C   79 LYS cc_start: 0.7550 (pttt) cc_final: 0.7296 (pttm)
REVERT: C  187 GLU cc_start: 0.6409 (tm-30) cc_final: 0.5862 (tm-30)
REVERT: C  230 MET cc_start: 0.0586 (mtp) cc_final: 0.0308 (ttm)
REVERT: E   54 LEU cc_start: 0.8662 (mm) cc_final: 0.8401 (mt)
REVERT: E   66 LEU cc_start: 0.7700 (mm) cc_final: 0.7347 (mm)
REVERT: E   99 LYS cc_start: 0.8230 (tttt) cc_final: 0.7985 (tttt)
REVERT: E  143 LYS cc_start: 0.6883 (mtmm) cc_final: 0.6656 (mtmm)
REVERT: E  166 VAL cc_start: 0.9050 (m) cc_final: 0.8801 (p)
REVERT: E  251 MET cc_start: 0.7589 (mtp) cc_final: 0.7334 (mmm)
REVERT: E  259 TYR cc_start: 0.6897 (m-80) cc_final: 0.6587 (m-80)
REVERT: E  288 GLN cc_start: 0.7812 (mt0) cc_final: 0.7113 (mp10)
REVERT: E  338 GLU cc_start: 0.7122 (tp30) cc_final: 0.6453 (tp30)
REVERT: E  342 GLU cc_start: 0.7754 (tp30) cc_final: 0.7397 (tp30)
REVERT: E  343 TYR cc_start: 0.7119 (m-80) cc_final: 0.6823 (m-80)
REVERT: E  414 LYS cc_start: 0.7583 (mmmt) cc_final: 0.7146 (mmmt)
REVERT: E  430 LEU cc_start: 0.8336 (tt) cc_final: 0.8099 (tt)
REVERT: E  583 MET cc_start: 0.8725 (mtp) cc_final: 0.8475 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.1433
  time to fit residues: 44.0438
Evaluate side-chains
  201 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 129 optimal weight:    9.9990
   chunk 84 optimal weight:    0.6980
   chunk 131 optimal weight:    6.9990
   chunk 98 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
E 284 ASN
E 386 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.189678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.159393 restraints weight = 23594.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.164198 restraints weight = 14336.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.167497 restraints weight = 9732.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.169873 restraints weight = 7226.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.171577 restraints weight = 5728.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4385
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4385 r_free = 0.4385    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4385 r_free = 0.4385    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4385
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6044
moved from start:          0.4341

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= 0.144
  Angle     :  0.644   8.674  16547  Z= 0.336
  Chirality :  0.045   0.301   1896
  Planarity :  0.004   0.054   1892
  Dihedral  : 19.299 165.856   2087
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.93 %
    Favored  : 89.84 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.77 (0.22), residues: 1319
  helix: -1.24 (0.28), residues: 302
  sheet: -0.87 (0.30), residues: 318
  loop : -2.66 (0.21), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  83 
 TYR   0.014   0.001   TYR C 200 
 PHE   0.019   0.002   PHE B  27 
 TRP   0.015   0.002   TRP E 431 
 HIS   0.003   0.001   HIS E 386 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (12074)
  covalent geometry    : angle       0.64371 (16547)
  hydrogen bonds       : bond        0.03834 (  386)
  hydrogen bonds       : angle       5.94458 (  988)

*********************** 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
  223 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.394 
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    3 LYS cc_start: 0.7812 (ptpp) cc_final: 0.7317 (ptpp)
REVERT: A   24 ASP cc_start: 0.7256 (t0) cc_final: 0.6924 (t0)
REVERT: A   29 ASN cc_start: 0.5542 (m110) cc_final: 0.5264 (m110)
REVERT: A   49 ILE cc_start: 0.7159 (mt) cc_final: 0.6819 (mt)
REVERT: A   50 MET cc_start: 0.4407 (tmm) cc_final: 0.3965 (tmm)
REVERT: A   78 ILE cc_start: 0.8759 (mm) cc_final: 0.8472 (tp)
REVERT: A   86 LYS cc_start: 0.8121 (pttp) cc_final: 0.7236 (pttp)
REVERT: A  110 LYS cc_start: 0.8740 (tttt) cc_final: 0.8395 (tttp)
REVERT: A  116 LYS cc_start: 0.8419 (tptp) cc_final: 0.8215 (tptp)
REVERT: A  164 ASP cc_start: 0.7815 (t70) cc_final: 0.6313 (t0)
REVERT: A  165 LYS cc_start: 0.8770 (pttm) cc_final: 0.8531 (pttm)
REVERT: A  183 LYS cc_start: 0.8542 (tttt) cc_final: 0.8214 (tppt)
REVERT: A  244 TRP cc_start: 0.6876 (m100) cc_final: 0.6465 (m100)
REVERT: B   68 ILE cc_start: 0.8210 (mp) cc_final: 0.7783 (mp)
REVERT: B  145 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6883 (mm-30)
REVERT: B  156 HIS cc_start: 0.6702 (p90) cc_final: 0.6222 (p-80)
REVERT: B  158 LYS cc_start: 0.8127 (tptp) cc_final: 0.7832 (tppt)
REVERT: C   78 LEU cc_start: 0.7951 (mt) cc_final: 0.7652 (mt)
REVERT: C   79 LYS cc_start: 0.7716 (pttt) cc_final: 0.7473 (pttm)
REVERT: C  187 GLU cc_start: 0.6250 (tm-30) cc_final: 0.5803 (tm-30)
REVERT: C  230 MET cc_start: 0.0534 (mtp) cc_final: 0.0230 (ttm)
REVERT: E   29 LEU cc_start: 0.7936 (tp) cc_final: 0.7443 (mm)
REVERT: E   53 PHE cc_start: 0.6561 (p90) cc_final: 0.6085 (p90)
REVERT: E   54 LEU cc_start: 0.8566 (mm) cc_final: 0.8322 (mm)
REVERT: E   99 LYS cc_start: 0.8216 (tttt) cc_final: 0.7967 (tttt)
REVERT: E  123 GLU cc_start: 0.6756 (tm-30) cc_final: 0.6350 (tm-30)
REVERT: E  180 LEU cc_start: 0.7715 (mt) cc_final: 0.7427 (mt)
REVERT: E  181 ASP cc_start: 0.7465 (m-30) cc_final: 0.7046 (t0)
REVERT: E  209 ASN cc_start: 0.6794 (m-40) cc_final: 0.6574 (m-40)
REVERT: E  258 ASP cc_start: 0.7018 (p0) cc_final: 0.6689 (p0)
REVERT: E  288 GLN cc_start: 0.7742 (mt0) cc_final: 0.7046 (mp10)
REVERT: E  338 GLU cc_start: 0.6982 (tp30) cc_final: 0.6376 (tp30)
REVERT: E  342 GLU cc_start: 0.7625 (tp30) cc_final: 0.7245 (tp30)
REVERT: E  343 TYR cc_start: 0.7113 (m-80) cc_final: 0.6826 (m-80)
REVERT: E  353 MET cc_start: 0.6417 (ptt) cc_final: 0.6206 (ptp)
REVERT: E  414 LYS cc_start: 0.7556 (mmmt) cc_final: 0.7332 (mmmt)
REVERT: E  430 LEU cc_start: 0.8284 (tt) cc_final: 0.8034 (tt)
REVERT: E  433 LYS cc_start: 0.8416 (mtpt) cc_final: 0.7988 (ttmm)
REVERT: E  583 MET cc_start: 0.8713 (mtp) cc_final: 0.8482 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1328
  time to fit residues: 39.4238
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  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 111 optimal weight:    0.8980
   chunk 3 optimal weight:    0.3980
   chunk 116 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0170
   chunk 24 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.5818

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.191481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.161514 restraints weight = 23367.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.166289 restraints weight = 14139.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 71)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.169657 restraints weight = 9590.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.171889 restraints weight = 7065.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.173727 restraints weight = 5620.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.4399
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4405
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4405 r_free = 0.4405    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4405 r_free = 0.4405    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4405
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6008
moved from start:          0.4576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12074  Z= 0.138
  Angle     :  0.652   8.522  16547  Z= 0.339
  Chirality :  0.045   0.316   1896
  Planarity :  0.004   0.055   1892
  Dihedral  : 19.256 166.156   2087
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.01 %
    Favored  : 89.76 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.22), residues: 1319
  helix: -1.15 (0.28), residues: 303
  sheet: -0.77 (0.30), residues: 314
  loop : -2.61 (0.21), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  83 
 TYR   0.014   0.001   TYR C 200 
 PHE   0.023   0.002   PHE C 128 
 TRP   0.019   0.002   TRP E 431 
 HIS   0.002   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (12074)
  covalent geometry    : angle       0.65202 (16547)
  hydrogen bonds       : bond        0.03612 (  386)
  hydrogen bonds       : angle       5.84676 (  988)

*********************** 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
  225 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.471 
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: 0.7265 (t0) cc_final: 0.6936 (t0)
REVERT: A   49 ILE cc_start: 0.7110 (mt) cc_final: 0.6471 (mp)
REVERT: A   50 MET cc_start: 0.4411 (tmm) cc_final: 0.4176 (tmm)
REVERT: A   86 LYS cc_start: 0.8073 (pttp) cc_final: 0.7192 (pttp)
REVERT: A   91 LEU cc_start: 0.8237 (tp) cc_final: 0.8029 (tp)
REVERT: A  110 LYS cc_start: 0.8723 (tttt) cc_final: 0.8359 (tttp)
REVERT: A  164 ASP cc_start: 0.7824 (t70) cc_final: 0.6183 (t0)
REVERT: A  165 LYS cc_start: 0.8772 (pttm) cc_final: 0.8445 (pttm)
REVERT: A  183 LYS cc_start: 0.8544 (tttt) cc_final: 0.8179 (tppt)
REVERT: A  244 TRP cc_start: 0.6699 (m100) cc_final: 0.6138 (m100)
REVERT: B   26 ASN cc_start: 0.7692 (t0) cc_final: 0.7474 (t0)
REVERT: B   59 PHE cc_start: 0.7571 (t80) cc_final: 0.7307 (t80)
REVERT: B  156 HIS cc_start: 0.6637 (p90) cc_final: 0.6156 (p-80)
REVERT: B  158 LYS cc_start: 0.8128 (tptp) cc_final: 0.7825 (tppt)
REVERT: B  209 ARG cc_start: 0.7659 (ptp90) cc_final: 0.7391 (ptp90)
REVERT: C   78 LEU cc_start: 0.7921 (mt) cc_final: 0.7659 (mt)
REVERT: C  112 ARG cc_start: 0.7390 (ptm-80) cc_final: 0.6963 (ptm-80)
REVERT: C  187 GLU cc_start: 0.6339 (tm-30) cc_final: 0.5894 (tm-30)
REVERT: C  230 MET cc_start: 0.0320 (mtp) cc_final: 0.0008 (ttm)
REVERT: E   29 LEU cc_start: 0.7888 (tp) cc_final: 0.7452 (mm)
REVERT: E   53 PHE cc_start: 0.6641 (p90) cc_final: 0.6229 (p90)
REVERT: E   54 LEU cc_start: 0.8464 (mm) cc_final: 0.8199 (mt)
REVERT: E   66 LEU cc_start: 0.7682 (mm) cc_final: 0.7384 (mm)
REVERT: E   99 LYS cc_start: 0.8132 (tttt) cc_final: 0.7886 (tttt)
REVERT: E  123 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6173 (tm-30)
REVERT: E  209 ASN cc_start: 0.6828 (m-40) cc_final: 0.6592 (m-40)
REVERT: E  258 ASP cc_start: 0.6990 (p0) cc_final: 0.6615 (p0)
REVERT: E  288 GLN cc_start: 0.7727 (mt0) cc_final: 0.7217 (mt0)
REVERT: E  338 GLU cc_start: 0.7035 (tp30) cc_final: 0.6399 (tp30)
REVERT: E  342 GLU cc_start: 0.7638 (tp30) cc_final: 0.7339 (tp30)
REVERT: E  343 TYR cc_start: 0.7087 (m-80) cc_final: 0.6715 (m-80)
REVERT: E  353 MET cc_start: 0.6323 (ptt) cc_final: 0.6018 (ptp)
REVERT: E  414 LYS cc_start: 0.7315 (mmmt) cc_final: 0.6886 (mmmt)
REVERT: E  583 MET cc_start: 0.8688 (mtp) cc_final: 0.8410 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1381
  time to fit residues: 41.5022
Evaluate side-chains
  190 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 25 optimal weight:    0.1980
   chunk 69 optimal weight:    0.0050
   chunk 73 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0770
   chunk 47 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0970
   chunk 116 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.2350

-------------------------------------------------------------------------------
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 = 0.4650 r_free = 0.4650 target = 0.194254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.164856 restraints weight = 23508.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.169544 restraints weight = 14346.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.172878 restraints weight = 9772.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.175239 restraints weight = 7221.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.177024 restraints weight = 5704.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.4447
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4447
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4447 r_free = 0.4447    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4447 r_free = 0.4447    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4447
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5910
moved from start:          0.4880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12074  Z= 0.124
  Angle     :  0.649   8.475  16547  Z= 0.337
  Chirality :  0.045   0.259   1896
  Planarity :  0.004   0.055   1892
  Dihedral  : 19.214 166.682   2087
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.02 %
    Favored  : 90.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.22), residues: 1319
  helix: -0.88 (0.29), residues: 297
  sheet: -0.67 (0.30), residues: 316
  loop : -2.47 (0.21), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 248 
 TYR   0.035   0.001   TYR B  13 
 PHE   0.021   0.002   PHE C 128 
 TRP   0.013   0.001   TRP E 431 
 HIS   0.002   0.001   HIS E 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12074)
  covalent geometry    : angle       0.64884 (16547)
  hydrogen bonds       : bond        0.03375 (  386)
  hydrogen bonds       : angle       5.55757 (  988)

*********************** 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
  219 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.7262 (t0) cc_final: 0.6902 (t0)
REVERT: A   49 ILE cc_start: 0.7032 (mt) cc_final: 0.6482 (mp)
REVERT: A   55 ASP cc_start: 0.4906 (p0) cc_final: 0.4448 (p0)
REVERT: A  164 ASP cc_start: 0.7753 (t70) cc_final: 0.5928 (t0)
REVERT: A  165 LYS cc_start: 0.8678 (pttm) cc_final: 0.8346 (pttm)
REVERT: A  183 LYS cc_start: 0.8552 (tttt) cc_final: 0.8347 (tppt)
REVERT: A  244 TRP cc_start: 0.6436 (m100) cc_final: 0.5972 (m100)
REVERT: B    1 MET cc_start: 0.4355 (tpp) cc_final: 0.4135 (tpp)
REVERT: B   16 ARG cc_start: 0.7886 (ttm170) cc_final: 0.7579 (ttm-80)
REVERT: B  156 HIS cc_start: 0.6658 (p90) cc_final: 0.6123 (p-80)
REVERT: B  158 LYS cc_start: 0.8067 (tptp) cc_final: 0.7795 (tppt)
REVERT: B  209 ARG cc_start: 0.7646 (ptp90) cc_final: 0.7229 (ptp90)
REVERT: B  214 MET cc_start: 0.7191 (mtm) cc_final: 0.6578 (mtp)
REVERT: B  215 GLU cc_start: 0.7161 (pm20) cc_final: 0.6835 (pm20)
REVERT: C   78 LEU cc_start: 0.7900 (mt) cc_final: 0.7653 (mt)
REVERT: C  143 ILE cc_start: 0.6200 (tt) cc_final: 0.5935 (tt)
REVERT: C  153 VAL cc_start: 0.5471 (t) cc_final: 0.5150 (m)
REVERT: C  230 MET cc_start: 0.0467 (mtp) cc_final: 0.0099 (ttm)
REVERT: E   29 LEU cc_start: 0.7757 (tp) cc_final: 0.7466 (mt)
REVERT: E   48 LYS cc_start: 0.6394 (mttt) cc_final: 0.6049 (mmtt)
REVERT: E   53 PHE cc_start: 0.6548 (p90) cc_final: 0.6153 (p90)
REVERT: E   66 LEU cc_start: 0.7229 (mm) cc_final: 0.6833 (mm)
REVERT: E   99 LYS cc_start: 0.7967 (tttt) cc_final: 0.7740 (tttt)
REVERT: E  123 GLU cc_start: 0.6752 (tm-30) cc_final: 0.6367 (tm-30)
REVERT: E  288 GLN cc_start: 0.7744 (mt0) cc_final: 0.7347 (mt0)
REVERT: E  338 GLU cc_start: 0.6594 (tp30) cc_final: 0.5994 (tp30)
REVERT: E  342 GLU cc_start: 0.7450 (tp30) cc_final: 0.7166 (tp30)
REVERT: E  343 TYR cc_start: 0.6946 (m-80) cc_final: 0.6573 (m-10)
REVERT: E  583 MET cc_start: 0.8703 (mtp) cc_final: 0.8398 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 219
  average time/residue: 0.1359
  time to fit residues: 39.9066
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  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 125 optimal weight:    8.9990
   chunk 22 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 129 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 124 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9980
   chunk 128 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
E 423 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.187077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.157148 restraints weight = 25758.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.161073 restraints weight = 17247.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.163856 restraints weight = 12649.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.165949 restraints weight = 9933.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.167430 restraints weight = 8230.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4345
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4345 r_free = 0.4345    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 = 0.4345 r_free = 0.4345    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4345
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6213
moved from start:          0.4825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  12074  Z= 0.271
  Angle     :  0.802   9.337  16547  Z= 0.420
  Chirality :  0.049   0.228   1896
  Planarity :  0.004   0.053   1892
  Dihedral  : 19.378 166.260   2087
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 21.09
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 12.43 %
    Favored  : 87.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.75 (0.22), residues: 1319
  helix: -1.33 (0.28), residues: 286
  sheet: -0.83 (0.29), residues: 328
  loop : -2.60 (0.21), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  83 
 TYR   0.026   0.002   TYR B  13 
 PHE   0.029   0.003   PHE A  12 
 TRP   0.017   0.002   TRP E 431 
 HIS   0.006   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 (12074)
  covalent geometry    : angle       0.80234 (16547)
  hydrogen bonds       : bond        0.05376 (  386)
  hydrogen bonds       : angle       6.30156 (  988)

*********************** 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
  220 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.398 
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: 0.7378 (t0) cc_final: 0.7071 (t0)
REVERT: A   49 ILE cc_start: 0.7159 (mt) cc_final: 0.6860 (mt)
REVERT: A  124 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7451 (tm-30)
REVERT: A  164 ASP cc_start: 0.7595 (t70) cc_final: 0.6239 (t0)
REVERT: A  165 LYS cc_start: 0.8789 (pttm) cc_final: 0.8536 (pttm)
REVERT: A  183 LYS cc_start: 0.8941 (tttt) cc_final: 0.8685 (tppt)
REVERT: B   16 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7542 (ttm-80)
REVERT: B   68 ILE cc_start: 0.7614 (pt) cc_final: 0.6963 (pt)
REVERT: B  156 HIS cc_start: 0.6723 (p90) cc_final: 0.6264 (p-80)
REVERT: B  176 GLU cc_start: 0.6908 (tp30) cc_final: 0.6693 (tp30)
REVERT: B  214 MET cc_start: 0.7084 (mtm) cc_final: 0.6798 (mtp)
REVERT: B  232 GLN cc_start: 0.6687 (pm20) cc_final: 0.6222 (pp30)
REVERT: C   78 LEU cc_start: 0.7461 (mt) cc_final: 0.7232 (mt)
REVERT: C  112 ARG cc_start: 0.7354 (ptm-80) cc_final: 0.7025 (ptm-80)
REVERT: C  230 MET cc_start: 0.1177 (mtp) cc_final: 0.0962 (ttm)
REVERT: E   29 LEU cc_start: 0.7837 (tp) cc_final: 0.7494 (mm)
REVERT: E   53 PHE cc_start: 0.6625 (p90) cc_final: 0.6405 (p90)
REVERT: E   54 LEU cc_start: 0.8560 (mm) cc_final: 0.8273 (mt)
REVERT: E   66 LEU cc_start: 0.7560 (mm) cc_final: 0.7220 (mm)
REVERT: E   99 LYS cc_start: 0.8113 (tttt) cc_final: 0.7868 (tttt)
REVERT: E  123 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6367 (tm-30)
REVERT: E  181 ASP cc_start: 0.7131 (m-30) cc_final: 0.6735 (t0)
REVERT: E  288 GLN cc_start: 0.7893 (mt0) cc_final: 0.7339 (mp10)
REVERT: E  338 GLU cc_start: 0.6888 (tp30) cc_final: 0.6245 (tp30)
REVERT: E  342 GLU cc_start: 0.7676 (tp30) cc_final: 0.7339 (tp30)
REVERT: E  343 TYR cc_start: 0.7060 (m-80) cc_final: 0.6798 (m-80)
REVERT: E  353 MET cc_start: 0.6850 (ptt) cc_final: 0.6611 (ptp)
REVERT: E  583 MET cc_start: 0.8690 (mtp) cc_final: 0.8441 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.1380
  time to fit residues: 40.2796
Evaluate side-chains
  194 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   chunk 6 optimal weight:    0.8980
   chunk 95 optimal weight:    0.0670
   chunk 36 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0010
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.4924

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

Flipped N/Q/H residues before XYZ refinement:
C 152 ASN
C 184 GLN
** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 423 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.193208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.164701 restraints weight = 26444.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.168567 restraints weight = 17755.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.171274 restraints weight = 13026.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.173440 restraints weight = 10247.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.175005 restraints weight = 8452.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.4442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6015
moved from start:          0.5049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12074  Z= 0.138
  Angle     :  0.680   9.237  16547  Z= 0.353
  Chirality :  0.046   0.220   1896
  Planarity :  0.004   0.053   1892
  Dihedral  : 19.401 168.031   2087
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.33 %
    Favored  : 90.45 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.22), residues: 1319
  helix: -1.22 (0.28), residues: 309
  sheet: -0.77 (0.31), residues: 303
  loop : -2.39 (0.22), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 209 
 TYR   0.017   0.001   TYR B  13 
 PHE   0.024   0.002   PHE C 128 
 TRP   0.014   0.001   TRP E 431 
 HIS   0.004   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (12074)
  covalent geometry    : angle       0.68008 (16547)
  hydrogen bonds       : bond        0.03666 (  386)
  hydrogen bonds       : angle       5.82752 (  988)

********************** 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
  216 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.7200 (t0) cc_final: 0.6875 (t0)
REVERT: A   50 MET cc_start: 0.4369 (tpt) cc_final: 0.3718 (tmm)
REVERT: A  162 GLU cc_start: 0.6702 (pm20) cc_final: 0.6322 (pm20)
REVERT: A  164 ASP cc_start: 0.7500 (t70) cc_final: 0.6016 (t0)
REVERT: A  165 LYS cc_start: 0.8699 (pttm) cc_final: 0.8360 (ptpt)
REVERT: A  183 LYS cc_start: 0.8893 (tttt) cc_final: 0.8689 (tppt)
REVERT: B   16 ARG cc_start: 0.7746 (ttm170) cc_final: 0.7480 (ttm-80)
REVERT: B   26 ASN cc_start: 0.7702 (t0) cc_final: 0.7437 (t0)
REVERT: B  156 HIS cc_start: 0.6692 (p90) cc_final: 0.6233 (p-80)
REVERT: B  214 MET cc_start: 0.6730 (mtm) cc_final: 0.6356 (mtp)
REVERT: C  112 ARG cc_start: 0.7074 (ptm-80) cc_final: 0.6821 (ptm-80)
REVERT: C  187 GLU cc_start: 0.6351 (tm-30) cc_final: 0.6125 (tm-30)
REVERT: C  230 MET cc_start: 0.1333 (mtp) cc_final: 0.1077 (ttm)
REVERT: E   29 LEU cc_start: 0.7667 (tp) cc_final: 0.7448 (mt)
REVERT: E   54 LEU cc_start: 0.8452 (mm) cc_final: 0.8229 (mt)
REVERT: E   66 LEU cc_start: 0.7020 (mm) cc_final: 0.6622 (mm)
REVERT: E  123 GLU cc_start: 0.6815 (tm-30) cc_final: 0.5296 (tm-30)
REVERT: E  181 ASP cc_start: 0.7064 (m-30) cc_final: 0.6786 (t0)
REVERT: E  194 SER cc_start: 0.7914 (t) cc_final: 0.7613 (p)
REVERT: E  233 ILE cc_start: 0.6643 (mt) cc_final: 0.6360 (mt)
REVERT: E  288 GLN cc_start: 0.7581 (mt0) cc_final: 0.7064 (mp10)
REVERT: E  338 GLU cc_start: 0.6361 (tp30) cc_final: 0.5851 (tp30)
REVERT: E  342 GLU cc_start: 0.7282 (tp30) cc_final: 0.6901 (tp30)
REVERT: E  343 TYR cc_start: 0.6964 (m-80) cc_final: 0.6695 (m-10)
REVERT: E  353 MET cc_start: 0.6501 (ptt) cc_final: 0.6228 (ptp)
REVERT: E  433 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7541 (mtpp)
REVERT: E  583 MET cc_start: 0.8690 (mtp) cc_final: 0.8425 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.1382
  time to fit residues: 39.9104
Evaluate side-chains
  185 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 134 optimal weight:    9.9990
   chunk 40 optimal weight:    0.7980
   chunk 13 optimal weight:    8.9990
   chunk 41 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0870
   chunk 77 optimal weight:    2.9990
   chunk 130 optimal weight:    0.5980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
B 181 ASN
C 152 ASN
** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.192550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.163991 restraints weight = 26356.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.167956 restraints weight = 17613.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.170678 restraints weight = 12871.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 66)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.172760 restraints weight = 10109.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.174147 restraints weight = 8351.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.4431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6034
moved from start:          0.5138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12074  Z= 0.141
  Angle     :  0.684   8.415  16547  Z= 0.356
  Chirality :  0.046   0.250   1896
  Planarity :  0.004   0.055   1892
  Dihedral  : 19.305 167.072   2087
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 10.08 %
    Favored  : 89.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.22), residues: 1319
  helix: -1.18 (0.28), residues: 310
  sheet: -0.79 (0.29), residues: 321
  loop : -2.43 (0.22), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 140 
 TYR   0.013   0.001   TYR B  13 
 PHE   0.036   0.002   PHE A  12 
 TRP   0.027   0.002   TRP E 431 
 HIS   0.004   0.001   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (12074)
  covalent geometry    : angle       0.68431 (16547)
  hydrogen bonds       : bond        0.03724 (  386)
  hydrogen bonds       : angle       5.70659 (  988)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2218.62 seconds
wall clock time: 39 minutes 3.94 seconds (2343.94 seconds total)