Starting phenix.real_space_refine
on Wed Sep 17 19:39:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n0y_48798/09_2025/9n0y_48798.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n0y_48798/09_2025/9n0y_48798.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n0y_48798/09_2025/9n0y_48798.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n0y_48798/09_2025/9n0y_48798.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n0y_48798/09_2025/9n0y_48798.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n0y_48798/09_2025/9n0y_48798.cif"
  }
  resolution = 3.71
  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=   0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    6824      2.51       5
     N    1846      2.21       5
     O    2060      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10792
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 4521
          Classifications: {'peptide': 580}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 553}
    Chain: "B"
      Number of atoms: 3594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3594
          Classifications: {'peptide': 439}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 423}
    Chain: "C"
      Number of atoms: 2504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2504
          Classifications: {'peptide': 309}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 295}
    Chain: "D"
      Number of atoms: 173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 173
          Classifications: {'peptide': 22}
          Link IDs: {'PTRANS': 2, 'TRANS': 19}
  Time building chain proxies: 2.57, per 1000 atoms: 0.24
  Number of scatterers: 10792
  At special positions: 0
  Unit cell: (107.73, 106.02, 124.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    2060      8.00
     N    1846      7.00
     C    6824      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: 0.99
  Conformation dependent library (CDL) restraints added in 423.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2590

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 14 sheets defined
      49.3% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 21
      removed outlier: 3.743A  pdb=" N   ASP A  18 " --> pdb=" O   ALA A  14 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLU A  19 " --> pdb=" O   VAL A  15 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A  20 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ARG A  21 " --> pdb=" O   ILE A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 33
    Processing helix  chain 'A' and resid 34 through 43
      removed outlier: 3.511A  pdb=" N   ILE A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 51
    Processing helix  chain 'A' and resid 51 through 57
      removed outlier: 4.392A  pdb=" N   ASP A  57 " --> pdb=" O   PRO A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 75
      removed outlier: 3.846A  pdb=" N   GLU A  71 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 88
    Processing helix  chain 'A' and resid 89 through 97
      removed outlier: 3.519A  pdb=" N   LEU A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 117
      removed outlier: 3.993A  pdb=" N   HIS A 117 " --> pdb=" O   ARG A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 136
      removed outlier: 4.955A  pdb=" N   VAL A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      Proline residue:  A 130  - end of helix
    Processing helix  chain 'A' and resid 140 through 148
      removed outlier: 3.787A  pdb=" N   ARG A 144 " --> pdb=" O   TRP A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 3.584A  pdb=" N   CYS A 154 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 174
    Processing helix  chain 'A' and resid 178 through 196
      removed outlier: 3.889A  pdb=" N   ARG A 182 " --> pdb=" O   THR A 178 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   LYS A 188 " --> pdb=" O   ALA A 184 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   GLY A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   GLU A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   VAL A 195 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A 196 " --> pdb=" O   PHE A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 214
      removed outlier: 4.642A  pdb=" N   ILE A 206 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
      Proline residue:  A 207  - end of helix
    Processing helix  chain 'A' and resid 220 through 233
      removed outlier: 4.026A  pdb=" N   ALA A 224 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   VAL A 225 " --> pdb=" O   ARG A 221 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   GLU A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 252
    Processing helix  chain 'A' and resid 256 through 265
      removed outlier: 3.805A  pdb=" N   ARG A 260 " --> pdb=" O   SER A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 292
      Proline residue:  A 276  - end of helix
      removed outlier: 5.401A  pdb=" N   VAL A 284 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
    Processing helix  chain 'A' and resid 295 through 305
      removed outlier: 4.070A  pdb=" N   ARG A 299 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 311
    Processing helix  chain 'A' and resid 317 through 334
      removed outlier: 4.933A  pdb=" N   LEU A 327 " --> pdb=" O   MET A 323 " (cutoff:3.500A)
      Proline residue:  A 328  - end of helix
    Processing helix  chain 'A' and resid 338 through 347
      removed outlier: 3.685A  pdb=" N   LYS A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   SER A 347 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 351
      removed outlier: 3.570A  pdb=" N   GLY A 351 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 348 through 351'
    Processing helix  chain 'A' and resid 352 through 373
      removed outlier: 7.187A  pdb=" N   LYS A 358 " --> pdb=" O   PRO A 354 " (cutoff:3.500A)
      removed outlier: 9.154A  pdb=" N   ASP A 359 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   ASN A 360 " --> pdb=" O   LEU A 356 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   LEU A 366 " --> pdb=" O   ILE A 362 " (cutoff:3.500A)
      Proline residue:  A 367  - end of helix
    Processing helix  chain 'A' and resid 377 through 387
      removed outlier: 3.906A  pdb=" N   ARG A 381 " --> pdb=" O   CYS A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 396
      removed outlier: 3.779A  pdb=" N   VAL A 394 " --> pdb=" O   CYS A 390 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLY A 396 " --> pdb=" O   ASN A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 412
      removed outlier: 4.475A  pdb=" N   SER A 403 " --> pdb=" O   GLN A 399 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   LEU A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
      Proline residue:  A 406  - end of helix
    Processing helix  chain 'A' and resid 416 through 435
      removed outlier: 4.038A  pdb=" N   ARG A 420 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
      Proline residue:  A 428  - end of helix
    Processing helix  chain 'A' and resid 435 through 443
    Processing helix  chain 'A' and resid 443 through 452
      removed outlier: 4.102A  pdb=" N   CYS A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   MET A 448 " --> pdb=" O   ASN A 444 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   VAL A 452 " --> pdb=" O   MET A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 474
      removed outlier: 3.516A  pdb=" N   LYS A 467 " --> pdb=" O   THR A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 482
    Processing helix  chain 'A' and resid 482 through 490
      removed outlier: 4.359A  pdb=" N   VAL A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 510
      removed outlier: 3.839A  pdb=" N   ARG A 498 " --> pdb=" O   ASN A 494 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   GLU A 510 " --> pdb=" O   ASN A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 529
      removed outlier: 4.677A  pdb=" N   LEU A 522 " --> pdb=" O   THR A 518 " (cutoff:3.500A)
      Proline residue:  A 523  - end of helix
    Processing helix  chain 'A' and resid 533 through 548
      removed outlier: 3.755A  pdb=" N   ARG A 537 " --> pdb=" O   VAL A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 551
      No H-bonds generated for 'chain 'A' and resid 549 through 551'
    Processing helix  chain 'A' and resid 552 through 559
    Processing helix  chain 'A' and resid 559 through 568
      removed outlier: 3.581A  pdb=" N   ILE A 563 " --> pdb=" O   GLU A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 586
    Processing helix  chain 'B' and resid 26 through 30
      removed outlier: 3.690A  pdb=" N   ASP B  29 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE B  30 " --> pdb=" O   GLU B  27 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 26 through 30'
    Processing helix  chain 'B' and resid 281 through 286
    Processing helix  chain 'B' and resid 326 through 330
    Processing helix  chain 'B' and resid 332 through 338
    Processing helix  chain 'B' and resid 411 through 413
      No H-bonds generated for 'chain 'B' and resid 411 through 413'
    Processing helix  chain 'C' and resid 2 through 18
    Processing helix  chain 'C' and resid 24 through 40
    Processing helix  chain 'C' and resid 61 through 72
    Processing helix  chain 'C' and resid 92 through 107
    Processing helix  chain 'C' and resid 120 through 127
    Processing helix  chain 'C' and resid 128 through 138
    Processing helix  chain 'C' and resid 140 through 151
      removed outlier: 3.798A  pdb=" N   ASP C 151 " --> pdb=" O   THR C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 183
      removed outlier: 3.782A  pdb=" N   ILE C 180 " --> pdb=" O   THR C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 193 through 201
    Processing helix  chain 'C' and resid 221 through 232
    Processing helix  chain 'C' and resid 264 through 268
    Processing helix  chain 'D' and resid 77 through 81
    Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13
      removed outlier: 3.612A  pdb=" N   GLN B 443 " --> pdb=" O   CYS B  13 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 36
      removed outlier: 3.606A  pdb=" N   GLU B  35 " --> pdb=" O   ALA B  44 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   VAL B  52 " --> pdb=" O   THR B  76 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   THR B  76 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ILE B  54 " --> pdb=" O   TYR B  74 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 114
      removed outlier: 3.860A  pdb=" N   LEU B 111 " --> pdb=" O   TRP B 122 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   SER B 113 " --> pdb=" O   LYS B 120 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ILE B 119 " --> pdb=" O   PHE B 172 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG B 170 " --> pdb=" O   LEU B 121 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 124 through 132
      removed outlier: 3.519A  pdb=" N   SER B 125 " --> pdb=" O   GLU B 165 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   LYS B 129 " --> pdb=" O   ASP B 161 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   ASP B 161 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 185
      removed outlier: 3.633A  pdb=" N   SER B 184 " --> pdb=" O   LEU B 193 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TYR B 192 " --> pdb=" O   TRP B 203 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER B 194 " --> pdb=" O   ASN B 201 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   VAL B 215 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 210 through 211
    Processing sheet with id=AA7, first strand: chain 'B' and resid 251 through 252
      removed outlier: 3.554A  pdb=" N   PHE B 269 " --> pdb=" O   ILE B 251 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 291 through 293
    Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 349
      removed outlier: 3.568A  pdb=" N   CYS B 349 " --> pdb=" O   MET B 358 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   MET B 358 " --> pdb=" O   CYS B 349 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   MET B 368 " --> pdb=" O   ILE B 377 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE B 377 " --> pdb=" O   MET B 368 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 397 through 398
      removed outlier: 3.617A  pdb=" N   CYS B 398 " --> pdb=" O   ILE B 408 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'C' and resid 52 through 53
    Processing sheet with id=AB3, first strand: chain 'C' and resid 80 through 82
      removed outlier: 6.368A  pdb=" N   TYR C  80 " --> pdb=" O   THR C 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 159
      removed outlier: 6.063A  pdb=" N   PHE C 164 " --> pdb=" O   SER C 238 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 210 through 211

    402 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.71

  Time building geometry restraints manager: 1.29 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: 3587
        1.34 -     1.46: 2187
        1.46 -     1.58: 5146
        1.58 -     1.70: 0
        1.70 -     1.82: 91
  Bond restraints: 11011
  Sorted by residual:
  bond pdb=" N   ILE A 482 "
       pdb=" CA  ILE A 482 "
    ideal  model  delta    sigma   weight residual
    1.459  1.503 -0.044 1.25e-02 6.40e+03 1.26e+01
  bond pdb=" N   ILE A 483 "
       pdb=" CA  ILE A 483 "
    ideal  model  delta    sigma   weight residual
    1.461  1.501 -0.040 1.23e-02 6.61e+03 1.07e+01
  bond pdb=" N   TYR D  67 "
       pdb=" CA  TYR D  67 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.034 1.22e-02 6.72e+03 7.63e+00
  bond pdb=" N   ASP D  66 "
       pdb=" CA  ASP D  66 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.035 1.27e-02 6.20e+03 7.44e+00
  bond pdb=" N   TYR D  72 "
       pdb=" CA  TYR D  72 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.27e-02 6.20e+03 6.72e+00
  ... (remaining 11006 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.60: 14856
        3.60 -     7.20: 65
        7.20 -    10.81: 2
       10.81 -    14.41: 1
       14.41 -    18.01: 1
  Bond angle restraints: 14925
  Sorted by residual:
  angle pdb=" N   PHE B 442 "
        pdb=" CA  PHE B 442 "
        pdb=" C   PHE B 442 "
      ideal   model   delta    sigma   weight residual
     109.96   91.95   18.01 1.49e+00 4.50e-01 1.46e+02
  angle pdb=" C   PHE B 442 "
        pdb=" CA  PHE B 442 "
        pdb=" CB  PHE B 442 "
      ideal   model   delta    sigma   weight residual
     110.16  121.00  -10.84 1.44e+00 4.82e-01 5.67e+01
  angle pdb=" C   SER B  89 "
        pdb=" N   LEU B  90 "
        pdb=" CA  LEU B  90 "
      ideal   model   delta    sigma   weight residual
     121.90  115.20    6.70 1.26e+00 6.30e-01 2.83e+01
  angle pdb=" N   PRO D  84 "
        pdb=" CA  PRO D  84 "
        pdb=" C   PRO D  84 "
      ideal   model   delta    sigma   weight residual
     112.47  120.50   -8.03 2.06e+00 2.36e-01 1.52e+01
  angle pdb=" CA  MET D  71 "
        pdb=" C   MET D  71 "
        pdb=" O   MET D  71 "
      ideal   model   delta    sigma   weight residual
     121.67  118.18    3.49 9.30e-01 1.16e+00 1.41e+01
  ... (remaining 14920 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 6039
       17.99 -    35.98: 543
       35.98 -    53.98: 93
       53.98 -    71.97: 18
       71.97 -    89.96: 12
  Dihedral angle restraints: 6705
    sinusoidal: 2724
      harmonic: 3981
  Sorted by residual:
  dihedral pdb=" CA  VAL D  83 "
           pdb=" C   VAL D  83 "
           pdb=" N   PRO D  84 "
           pdb=" CA  PRO D  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.36  -24.64     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  ILE B 185 "
           pdb=" C   ILE B 185 "
           pdb=" N   ASN B 186 "
           pdb=" CA  ASN B 186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.15  -23.85     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" CA  PHE B 242 "
           pdb=" C   PHE B 242 "
           pdb=" N   VAL B 243 "
           pdb=" CA  VAL B 243 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.12  -22.88     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 6702 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1037
       0.034 -    0.068: 428
       0.068 -    0.102: 155
       0.102 -    0.136: 50
       0.136 -    0.170: 14
  Chirality restraints: 1684
  Sorted by residual:
  chirality pdb=" CA  PRO D  84 "
            pdb=" N   PRO D  84 "
            pdb=" C   PRO D  84 "
            pdb=" CB  PRO D  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.20e-01
  chirality pdb=" CB  VAL A 452 "
            pdb=" CA  VAL A 452 "
            pdb=" CG1 VAL A 452 "
            pdb=" CG2 VAL A 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.15e-01
  chirality pdb=" CB  ILE B 441 "
            pdb=" CA  ILE B 441 "
            pdb=" CG1 ILE B 441 "
            pdb=" CG2 ILE B 441 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.17 2.00e-01 2.50e+01 7.04e-01
  ... (remaining 1681 not shown)

  Planarity restraints: 1932
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 387 "    0.027 5.00e-02 4.00e+02   4.02e-02 2.59e+00
        pdb=" N   PRO B 388 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 388 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 388 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 366 "    0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO A 367 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 367 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 367 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 234 "   -0.011 2.00e-02 2.50e+03   1.18e-02 2.42e+00
        pdb=" CG  PHE B 234 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 234 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 234 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 234 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 234 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 234 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1929 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.49: 73
        2.49 -     3.09: 8049
        3.09 -     3.69: 15676
        3.69 -     4.30: 22437
        4.30 -     4.90: 37146
  Nonbonded interactions: 83381
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C 117 "
            pdb=" NE2 HIS C 167 "
     model   vdw
     1.884 3.120
  nonbonded pdb=" O   ILE A 397 "
            pdb=" OG  SER A 401 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   GLY A 357 "
            pdb=" OG1 THR A 361 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   LYS B 393 "
            pdb=" NH1 ARG B 395 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" ND2 ASN B 135 "
            pdb=" O   ARG B 153 "
     model   vdw
     2.295 3.120
  ... (remaining 83376 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.320
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.490
  Find NCS groups from input model:        0.050
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11011  Z= 0.209
  Angle     :  0.705  18.008  14925  Z= 0.411
  Chirality :  0.045   0.170   1684
  Planarity :  0.004   0.040   1932
  Dihedral  : 14.462  89.959   4115
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.99 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.71 (0.22), residues: 1342
  helix: -1.21 (0.21), residues: 576
  sheet: -4.24 (0.32), residues: 189
  loop : -3.08 (0.24), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 181 
 TYR   0.013   0.001   TYR B 244 
 PHE   0.026   0.002   PHE B 234 
 TRP   0.017   0.001   TRP C 143 
 HIS   0.004   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (11011)
  covalent geometry    : angle       0.70539 (14925)
  hydrogen bonds       : bond        0.15702 (  402)
  hydrogen bonds       : angle       6.60221 ( 1164)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 VAL cc_start: 0.9060 (t) cc_final: 0.8785 (p)
REVERT: B  395 ARG cc_start: 0.8613 (mmt-90) cc_final: 0.7994 (mpt180)
REVERT: C    9 GLU cc_start: 0.7065 (tp30) cc_final: 0.6718 (tp30)
REVERT: C   89 ARG cc_start: 0.7980 (mtm180) cc_final: 0.7600 (mtt90)
REVERT: C   92 TYR cc_start: 0.8110 (m-80) cc_final: 0.7806 (m-80)
REVERT: C  195 MET cc_start: 0.7304 (pmm) cc_final: 0.6993 (pmm)
REVERT: C  245 MET cc_start: 0.8117 (tpp) cc_final: 0.7719 (tpp)
REVERT: C  260 PHE cc_start: 0.8698 (t80) cc_final: 0.7802 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1188
  time to fit residues: 31.1026
Evaluate side-chains
  112 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.4980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0170
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.5024

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
B 109 GLN
B 240 ASN
B 277 ASN
B 363 ASN
C 255 ASN
** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.142568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.095331 restraints weight = 17115.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.096865 restraints weight = 12488.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.097057 restraints weight = 9947.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.097232 restraints weight = 9872.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.097471 restraints weight = 9613.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11011  Z= 0.172
  Angle     :  0.637   8.304  14925  Z= 0.333
  Chirality :  0.045   0.159   1684
  Planarity :  0.005   0.045   1932
  Dihedral  :  5.203  25.945   1468
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.68 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.92 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.65 (0.23), residues: 1342
  helix: -0.17 (0.22), residues: 571
  sheet: -4.06 (0.35), residues: 163
  loop : -2.66 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 318 
 TYR   0.014   0.001   TYR B  74 
 PHE   0.031   0.002   PHE A 538 
 TRP   0.008   0.001   TRP A 417 
 HIS   0.008   0.001   HIS C 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (11011)
  covalent geometry    : angle       0.63702 (14925)
  hydrogen bonds       : bond        0.04027 (  402)
  hydrogen bonds       : angle       5.25622 ( 1164)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ARG cc_start: 0.8617 (ttp-110) cc_final: 0.8308 (ttm170)
REVERT: B  395 ARG cc_start: 0.8410 (mmt-90) cc_final: 0.8070 (mpt180)
REVERT: C   89 ARG cc_start: 0.8256 (mtm180) cc_final: 0.8008 (mtt90)
REVERT: C  143 TRP cc_start: 0.8144 (t60) cc_final: 0.7937 (t60)
REVERT: C  245 MET cc_start: 0.8019 (tpp) cc_final: 0.7792 (tpp)
REVERT: C  260 PHE cc_start: 0.8550 (t80) cc_final: 0.7888 (t80)
  outliers start: 20
  outliers final: 12
  residues processed: 135
  average time/residue: 0.0902
  time to fit residues: 18.3502
Evaluate side-chains
  119 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain C residue   32 CYS
Chi-restraints excluded: chain C residue   78 THR
Chi-restraints excluded: chain C residue  105 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 96 optimal weight:    9.9990
   chunk 123 optimal weight:    9.9990
   chunk 100 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 1 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0000
   chunk 57 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.6788

-------------------------------------------------------------------------------
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 = 0.3907 r_free = 0.3907 target = 0.144850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.099546 restraints weight = 16922.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.099992 restraints weight = 11554.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.100089 restraints weight = 9246.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.100258 restraints weight = 9310.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.100507 restraints weight = 8956.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11011  Z= 0.113
  Angle     :  0.567   7.880  14925  Z= 0.297
  Chirality :  0.043   0.151   1684
  Planarity :  0.004   0.045   1932
  Dihedral  :  4.917  23.858   1468
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.49 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.17 (0.23), residues: 1342
  helix:  0.25 (0.22), residues: 574
  sheet: -4.09 (0.34), residues: 159
  loop : -2.36 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 318 
 TYR   0.011   0.001   TYR C 130 
 PHE   0.028   0.001   PHE A 538 
 TRP   0.006   0.001   TRP A 417 
 HIS   0.024   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (11011)
  covalent geometry    : angle       0.56661 (14925)
  hydrogen bonds       : bond        0.03469 (  402)
  hydrogen bonds       : angle       4.93393 ( 1164)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  528 MET cc_start: 0.8595 (mmt) cc_final: 0.8325 (mmt)
REVERT: B  341 CYS cc_start: 0.8084 (m) cc_final: 0.7761 (m)
REVERT: B  395 ARG cc_start: 0.8375 (mmt-90) cc_final: 0.8115 (mpt180)
REVERT: B  439 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8490 (tt)
REVERT: C   87 VAL cc_start: 0.6441 (OUTLIER) cc_final: 0.6198 (m)
REVERT: C  143 TRP cc_start: 0.8092 (t60) cc_final: 0.7884 (t60)
REVERT: C  260 PHE cc_start: 0.8533 (t80) cc_final: 0.7837 (t80)
REVERT: D   72 TYR cc_start: 0.4725 (OUTLIER) cc_final: 0.4105 (p90)
  outliers start: 20
  outliers final: 9
  residues processed: 139
  average time/residue: 0.0934
  time to fit residues: 19.3483
Evaluate side-chains
  119 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain D residue   72 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 117 optimal weight:   10.0000
   chunk 60 optimal weight:    0.0370
   chunk 47 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0980
   chunk 124 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.6060

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.145867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.097725 restraints weight = 17042.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.099718 restraints weight = 13093.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.099958 restraints weight = 10771.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.100610 restraints weight = 9733.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.100884 restraints weight = 9441.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11011  Z= 0.109
  Angle     :  0.556   8.205  14925  Z= 0.290
  Chirality :  0.042   0.147   1684
  Planarity :  0.004   0.044   1932
  Dihedral  :  4.714  23.344   1468
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.40 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.83 (0.24), residues: 1342
  helix:  0.54 (0.23), residues: 574
  sheet: -3.89 (0.33), residues: 169
  loop : -2.14 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 257 
 TYR   0.014   0.001   TYR A 577 
 PHE   0.024   0.001   PHE A 538 
 TRP   0.005   0.001   TRP A 417 
 HIS   0.006   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (11011)
  covalent geometry    : angle       0.55572 (14925)
  hydrogen bonds       : bond        0.03160 (  402)
  hydrogen bonds       : angle       4.75029 ( 1164)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  528 MET cc_start: 0.8631 (mmt) cc_final: 0.8379 (mmt)
REVERT: B  341 CYS cc_start: 0.7908 (m) cc_final: 0.7578 (m)
REVERT: B  395 ARG cc_start: 0.8387 (mmt-90) cc_final: 0.8138 (mpt180)
REVERT: B  439 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8478 (tt)
REVERT: C  260 PHE cc_start: 0.8522 (t80) cc_final: 0.7798 (t80)
REVERT: D   72 TYR cc_start: 0.4393 (OUTLIER) cc_final: 0.3965 (p90)
  outliers start: 22
  outliers final: 12
  residues processed: 136
  average time/residue: 0.0884
  time to fit residues: 18.5045
Evaluate side-chains
  125 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain D residue   72 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 48 optimal weight:    8.9990
   chunk 19 optimal weight:    0.4980
   chunk 24 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 557 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.146066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.101549 restraints weight = 16863.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.101889 restraints weight = 11746.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.101817 restraints weight = 10195.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.102129 restraints weight = 10643.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.102350 restraints weight = 9443.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11011  Z= 0.109
  Angle     :  0.554   7.981  14925  Z= 0.284
  Chirality :  0.042   0.152   1684
  Planarity :  0.004   0.043   1932
  Dihedral  :  4.636  21.804   1468
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 17.32 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.64 (0.24), residues: 1342
  helix:  0.71 (0.23), residues: 570
  sheet: -3.72 (0.33), residues: 181
  loop : -2.00 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 171 
 TYR   0.019   0.001   TYR B  86 
 PHE   0.021   0.001   PHE A 538 
 TRP   0.009   0.001   TRP C 143 
 HIS   0.005   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (11011)
  covalent geometry    : angle       0.55362 (14925)
  hydrogen bonds       : bond        0.03062 (  402)
  hydrogen bonds       : angle       4.63065 ( 1164)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 CYS cc_start: 0.7874 (m) cc_final: 0.7530 (m)
REVERT: B  395 ARG cc_start: 0.8370 (mmt-90) cc_final: 0.8139 (mpt180)
REVERT: B  439 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8463 (tt)
REVERT: C  195 MET cc_start: 0.7439 (pmm) cc_final: 0.7179 (pmm)
REVERT: C  260 PHE cc_start: 0.8448 (t80) cc_final: 0.7828 (t80)
REVERT: D   72 TYR cc_start: 0.4415 (OUTLIER) cc_final: 0.3921 (p90)
  outliers start: 24
  outliers final: 16
  residues processed: 137
  average time/residue: 0.0873
  time to fit residues: 18.2512
Evaluate side-chains
  133 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  315 MET
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain D residue   72 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 126 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 201 ASN
B 240 ASN
** C 241 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 = 0.3887 r_free = 0.3887 target = 0.143464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.099571 restraints weight = 17165.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.100277 restraints weight = 14092.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.100437 restraints weight = 12337.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.100725 restraints weight = 11819.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.100808 restraints weight = 11257.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11011  Z= 0.154
  Angle     :  0.590   7.575  14925  Z= 0.305
  Chirality :  0.043   0.155   1684
  Planarity :  0.004   0.041   1932
  Dihedral  :  4.727  22.943   1468
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 18.23 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.24), residues: 1342
  helix:  0.71 (0.23), residues: 572
  sheet: -3.65 (0.34), residues: 182
  loop : -1.94 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  48 
 TYR   0.017   0.001   TYR B  86 
 PHE   0.019   0.001   PHE A 538 
 TRP   0.010   0.001   TRP C 143 
 HIS   0.007   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (11011)
  covalent geometry    : angle       0.58965 (14925)
  hydrogen bonds       : bond        0.03317 (  402)
  hydrogen bonds       : angle       4.72878 ( 1164)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
REVERT: A  426 TYR cc_start: 0.8761 (m-80) cc_final: 0.8522 (m-80)
REVERT: B  341 CYS cc_start: 0.7901 (m) cc_final: 0.7566 (m)
REVERT: B  395 ARG cc_start: 0.8405 (mmt-90) cc_final: 0.8159 (mpt180)
REVERT: B  439 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8327 (tt)
REVERT: C   85 ASP cc_start: 0.7306 (m-30) cc_final: 0.7058 (m-30)
REVERT: C  230 HIS cc_start: 0.7541 (m90) cc_final: 0.7316 (m90)
REVERT: C  260 PHE cc_start: 0.8394 (t80) cc_final: 0.7902 (t80)
REVERT: D   72 TYR cc_start: 0.4705 (OUTLIER) cc_final: 0.4148 (p90)
  outliers start: 29
  outliers final: 21
  residues processed: 131
  average time/residue: 0.0766
  time to fit residues: 15.7406
Evaluate side-chains
  130 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  160 MET
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  368 MET
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  301 THR
Chi-restraints excluded: chain D residue   72 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 127 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** C 241 HIS ** 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 = 0.3884 r_free = 0.3884 target = 0.143116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.098690 restraints weight = 17109.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.098487 restraints weight = 11794.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.098295 restraints weight = 9947.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.098518 restraints weight = 9955.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.098659 restraints weight = 9534.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11011  Z= 0.152
  Angle     :  0.586   8.244  14925  Z= 0.302
  Chirality :  0.043   0.156   1684
  Planarity :  0.004   0.040   1932
  Dihedral  :  4.762  22.857   1468
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.31 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.53 (0.24), residues: 1342
  helix:  0.74 (0.23), residues: 572
  sheet: -3.62 (0.34), residues: 175
  loop : -1.92 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 254 
 TYR   0.015   0.001   TYR B  86 
 PHE   0.018   0.001   PHE A 538 
 TRP   0.019   0.001   TRP C 250 
 HIS   0.005   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (11011)
  covalent geometry    : angle       0.58622 (14925)
  hydrogen bonds       : bond        0.03283 (  402)
  hydrogen bonds       : angle       4.72401 ( 1164)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  426 TYR cc_start: 0.8796 (m-80) cc_final: 0.8575 (m-80)
REVERT: B  341 CYS cc_start: 0.7944 (m) cc_final: 0.7579 (m)
REVERT: B  395 ARG cc_start: 0.8416 (mmt-90) cc_final: 0.8133 (mpt180)
REVERT: B  439 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8353 (tt)
REVERT: C   83 MET cc_start: 0.8703 (mmm) cc_final: 0.8080 (mmt)
REVERT: C   85 ASP cc_start: 0.7356 (m-30) cc_final: 0.7101 (m-30)
REVERT: C  218 TYR cc_start: 0.7940 (m-80) cc_final: 0.7623 (m-80)
REVERT: C  260 PHE cc_start: 0.8462 (t80) cc_final: 0.7905 (t80)
REVERT: D   72 TYR cc_start: 0.4611 (OUTLIER) cc_final: 0.4102 (p90)
  outliers start: 28
  outliers final: 21
  residues processed: 132
  average time/residue: 0.0924
  time to fit residues: 18.5663
Evaluate side-chains
  129 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  293 ASP
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  354 ASP
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  368 MET
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  301 THR
Chi-restraints excluded: chain D residue   72 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 119 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9980
   chunk 128 optimal weight:    6.9990
   chunk 124 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 64 optimal weight:    0.4980
   chunk 113 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 288 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 = 0.3898 r_free = 0.3898 target = 0.144131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.099595 restraints weight = 17052.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.099197 restraints weight = 11970.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.098981 restraints weight = 10258.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.100019 restraints weight = 10690.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.099848 restraints weight = 9650.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11011  Z= 0.129
  Angle     :  0.577   9.336  14925  Z= 0.294
  Chirality :  0.043   0.146   1684
  Planarity :  0.004   0.040   1932
  Dihedral  :  4.698  22.487   1468
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.39 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.24), residues: 1342
  helix:  0.80 (0.23), residues: 572
  sheet: -3.50 (0.34), residues: 185
  loop : -1.87 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 183 
 TYR   0.018   0.001   TYR A 577 
 PHE   0.016   0.001   PHE A 538 
 TRP   0.012   0.001   TRP C 143 
 HIS   0.005   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (11011)
  covalent geometry    : angle       0.57747 (14925)
  hydrogen bonds       : bond        0.03106 (  402)
  hydrogen bonds       : angle       4.64551 ( 1164)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 CYS cc_start: 0.7952 (m) cc_final: 0.7586 (m)
REVERT: B  395 ARG cc_start: 0.8431 (mmt-90) cc_final: 0.8163 (mpt180)
REVERT: B  439 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8274 (tt)
REVERT: C  143 TRP cc_start: 0.7990 (t60) cc_final: 0.7505 (t60)
REVERT: C  218 TYR cc_start: 0.8001 (m-80) cc_final: 0.7688 (m-80)
REVERT: C  260 PHE cc_start: 0.8473 (t80) cc_final: 0.7818 (t80)
REVERT: C  276 MET cc_start: 0.8377 (ttm) cc_final: 0.8116 (ttm)
REVERT: D   72 TYR cc_start: 0.4517 (OUTLIER) cc_final: 0.3994 (p90)
  outliers start: 27
  outliers final: 23
  residues processed: 132
  average time/residue: 0.0881
  time to fit residues: 17.7371
Evaluate side-chains
  133 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  559 GLU
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  354 ASP
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  368 MET
Chi-restraints excluded: chain B residue  422 THR
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  301 THR
Chi-restraints excluded: chain D residue   72 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 80 optimal weight:    0.0470
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 113 optimal weight:    0.5980
   chunk 56 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 132 optimal weight:   10.0000
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.6280

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

Flipped N/Q/H residues before XYZ refinement:
** C 241 HIS ** 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 = 0.3914 r_free = 0.3914 target = 0.145430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.097427 restraints weight = 16944.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.100050 restraints weight = 12844.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.100539 restraints weight = 9446.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.100592 restraints weight = 9231.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.100780 restraints weight = 9274.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11011  Z= 0.109
  Angle     :  0.572   8.587  14925  Z= 0.290
  Chirality :  0.042   0.156   1684
  Planarity :  0.004   0.038   1932
  Dihedral  :  4.622  21.649   1468
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 19.22 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.24), residues: 1342
  helix:  0.86 (0.23), residues: 574
  sheet: -3.38 (0.34), residues: 185
  loop : -1.81 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 144 
 TYR   0.020   0.001   TYR B  86 
 PHE   0.016   0.001   PHE A 538 
 TRP   0.011   0.001   TRP C 143 
 HIS   0.005   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (11011)
  covalent geometry    : angle       0.57201 (14925)
  hydrogen bonds       : bond        0.02965 (  402)
  hydrogen bonds       : angle       4.55444 ( 1164)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  489 MET cc_start: 0.7291 (tmm) cc_final: 0.6963 (tmm)
REVERT: B  341 CYS cc_start: 0.7948 (m) cc_final: 0.7561 (m)
REVERT: B  395 ARG cc_start: 0.8448 (mmt-90) cc_final: 0.8145 (mpt180)
REVERT: B  439 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8211 (tt)
REVERT: C  143 TRP cc_start: 0.7995 (t60) cc_final: 0.7516 (t60)
REVERT: C  218 TYR cc_start: 0.8093 (m-80) cc_final: 0.7784 (m-80)
REVERT: C  260 PHE cc_start: 0.8459 (t80) cc_final: 0.7778 (t80)
REVERT: D   72 TYR cc_start: 0.4516 (OUTLIER) cc_final: 0.4042 (p90)
  outliers start: 21
  outliers final: 17
  residues processed: 127
  average time/residue: 0.0919
  time to fit residues: 17.7998
Evaluate side-chains
  126 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  502 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  559 GLU
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  368 MET
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  301 THR
Chi-restraints excluded: chain D residue   72 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 124 optimal weight:    0.0770
   chunk 10 optimal weight:    4.9990
   chunk 118 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 89 optimal weight:    0.3980
   chunk 34 optimal weight:    0.0270
   chunk 85 optimal weight:    0.0770
   overall best weight:    0.2954

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

Flipped N/Q/H residues before XYZ refinement:
** C 241 HIS ** 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 = 0.3932 r_free = 0.3932 target = 0.146992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.100172 restraints weight = 16952.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.101706 restraints weight = 12187.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.101528 restraints weight = 9693.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.102072 restraints weight = 9674.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.102158 restraints weight = 9105.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11011  Z= 0.099
  Angle     :  0.566   9.406  14925  Z= 0.287
  Chirality :  0.042   0.141   1684
  Planarity :  0.004   0.038   1932
  Dihedral  :  4.461  21.125   1468
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 20.05 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.14 (0.24), residues: 1342
  helix:  0.97 (0.23), residues: 582
  sheet: -3.15 (0.37), residues: 175
  loop : -1.75 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 182 
 TYR   0.021   0.001   TYR B  86 
 PHE   0.015   0.001   PHE A 538 
 TRP   0.011   0.001   TRP C 143 
 HIS   0.005   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (11011)
  covalent geometry    : angle       0.56637 (14925)
  hydrogen bonds       : bond        0.02746 (  402)
  hydrogen bonds       : angle       4.41974 ( 1164)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  341 CYS cc_start: 0.7930 (m) cc_final: 0.7551 (m)
REVERT: B  395 ARG cc_start: 0.8454 (mmt-90) cc_final: 0.8155 (mpt180)
REVERT: C   83 MET cc_start: 0.8201 (mmt) cc_final: 0.7946 (mmm)
REVERT: C  143 TRP cc_start: 0.8009 (t60) cc_final: 0.7524 (t60)
REVERT: C  218 TYR cc_start: 0.8108 (m-80) cc_final: 0.7811 (m-80)
REVERT: C  260 PHE cc_start: 0.8433 (t80) cc_final: 0.7697 (t80)
REVERT: D   72 TYR cc_start: 0.4398 (OUTLIER) cc_final: 0.3938 (p90)
  outliers start: 18
  outliers final: 14
  residues processed: 123
  average time/residue: 0.0922
  time to fit residues: 17.3367
Evaluate side-chains
  122 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  559 GLU
Chi-restraints excluded: chain B residue   45 THR
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  368 MET
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain C residue  275 ILE
Chi-restraints excluded: chain C residue  301 THR
Chi-restraints excluded: chain D residue   72 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 132 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 65 optimal weight:    6.9990
   chunk 100 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 111 optimal weight:    0.6980
   chunk 63 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 97 optimal weight:    7.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** C 241 HIS ** 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 = 0.3916 r_free = 0.3916 target = 0.145800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.099558 restraints weight = 17097.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.100577 restraints weight = 12284.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.100349 restraints weight = 10614.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.100392 restraints weight = 10063.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.100566 restraints weight = 9641.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11011  Z= 0.114
  Angle     :  0.580   9.766  14925  Z= 0.292
  Chirality :  0.042   0.142   1684
  Planarity :  0.004   0.038   1932
  Dihedral  :  4.431  20.918   1468
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 19.88 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.10 (0.24), residues: 1342
  helix:  0.99 (0.23), residues: 581
  sheet: -3.08 (0.37), residues: 175
  loop : -1.72 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 498 
 TYR   0.023   0.001   TYR B  86 
 PHE   0.019   0.001   PHE A 369 
 TRP   0.010   0.001   TRP C 143 
 HIS   0.005   0.001   HIS A 479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (11011)
  covalent geometry    : angle       0.58019 (14925)
  hydrogen bonds       : bond        0.02844 (  402)
  hydrogen bonds       : angle       4.44459 ( 1164)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1932.89 seconds
wall clock time: 34 minutes 15.10 seconds (2055.10 seconds total)