Starting phenix.real_space_refine
on Sat Aug 23 00:30:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9axc_43932/08_2025/9axc_43932.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9axc_43932/08_2025/9axc_43932.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9axc_43932/08_2025/9axc_43932.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9axc_43932/08_2025/9axc_43932.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9axc_43932/08_2025/9axc_43932.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9axc_43932/08_2025/9axc_43932.map"
  }
  resolution = 4.16
  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=   0.000 sd=   0.008
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: 5
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    5566      2.51       5
     N    1479      2.21       5
     O    1568      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8677
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2120
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 2120
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 11, 'TRANS': 250}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2186
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 12, 'TRANS': 265}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2137
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 11, 'TRANS': 252}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2166
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 12, 'TRANS': 262}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'A1AHE': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'A1AHE': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.10, per 1000 atoms: 0.24
  Number of scatterers: 8677
  At special positions: 0
  Unit cell: (85.0935, 164.756, 65.178, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     F       4      9.00
     O    1568      8.00
     N    1479      7.00
     C    5566      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: 0.86
  Conformation dependent library (CDL) restraints added in 345.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2020

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 8 sheets defined
      50.6% alpha, 10.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 345 through 349
      removed outlier: 3.747A  pdb=" N   GLU A 348 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 399
      removed outlier: 3.911A  pdb=" N   LYS A 399 " --> pdb=" O   ALA A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 435
    Processing helix  chain 'A' and resid 441 through 462
      removed outlier: 3.578A  pdb=" N   LEU A 445 " --> pdb=" O   GLN A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 472
      No H-bonds generated for 'chain 'A' and resid 470 through 472'
    Processing helix  chain 'A' and resid 513 through 519
    Processing helix  chain 'A' and resid 526 through 544
      removed outlier: 3.719A  pdb=" N   ASP A 530 " --> pdb=" O   SER A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 563
    Processing helix  chain 'A' and resid 569 through 573
      removed outlier: 4.331A  pdb=" N   LYS A 572 " --> pdb=" O   ASP A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 589
      removed outlier: 3.553A  pdb=" N   LYS A 582 " --> pdb=" O   PRO A 578 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL A 589 " --> pdb=" O   VAL A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 596
      removed outlier: 3.759A  pdb=" N   GLU A 595 " --> pdb=" O   VAL A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 612
      removed outlier: 3.795A  pdb=" N   SER A 612 " --> pdb=" O   LEU A 608 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 59
      removed outlier: 3.757A  pdb=" N   LYS B  57 " --> pdb=" O   PHE B  53 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLN B  58 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 68
    Processing helix  chain 'B' and resid 104 through 116
    Processing helix  chain 'B' and resid 117 through 120
    Processing helix  chain 'B' and resid 150 through 159
      removed outlier: 3.784A  pdb=" N   VAL B 154 " --> pdb=" O   SER B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 184
    Processing helix  chain 'B' and resid 192 through 194
      No H-bonds generated for 'chain 'B' and resid 192 through 194'
    Processing helix  chain 'B' and resid 212 through 219
    Processing helix  chain 'B' and resid 231 through 236
    Processing helix  chain 'B' and resid 241 through 259
      removed outlier: 4.094A  pdb=" N   ASP B 245 " --> pdb=" O   SER B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 320
    Processing helix  chain 'B' and resid 331 through 342
      removed outlier: 3.821A  pdb=" N   GLN B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 357
    Processing helix  chain 'B' and resid 358 through 367
    Processing helix  chain 'B' and resid 370 through 380
      removed outlier: 3.585A  pdb=" N   TRP B 374 " --> pdb=" O   ASP B 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 398
      removed outlier: 3.803A  pdb=" N   ALA C 389 " --> pdb=" O   GLU C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 428 through 435
    Processing helix  chain 'C' and resid 441 through 462
    Processing helix  chain 'C' and resid 478 through 480
      No H-bonds generated for 'chain 'C' and resid 478 through 480'
    Processing helix  chain 'C' and resid 486 through 490
      removed outlier: 4.658A  pdb=" N   LEU C 489 " --> pdb=" O   ASP C 486 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 513 through 519
    Processing helix  chain 'C' and resid 526 through 544
      removed outlier: 3.828A  pdb=" N   ASP C 530 " --> pdb=" O   SER C 526 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 553 through 563
    Processing helix  chain 'C' and resid 569 through 573
      removed outlier: 3.698A  pdb=" N   LYS C 572 " --> pdb=" O   ASP C 569 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU C 573 " --> pdb=" O   LEU C 570 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 569 through 573'
    Processing helix  chain 'C' and resid 578 through 588
    Processing helix  chain 'C' and resid 598 through 613
    Processing helix  chain 'D' and resid 64 through 68
    Processing helix  chain 'D' and resid 104 through 114
    Processing helix  chain 'D' and resid 115 through 121
      removed outlier: 3.699A  pdb=" N   LEU D 118 " --> pdb=" O   LEU D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 159
    Processing helix  chain 'D' and resid 162 through 185
    Processing helix  chain 'D' and resid 192 through 194
      No H-bonds generated for 'chain 'D' and resid 192 through 194'
    Processing helix  chain 'D' and resid 212 through 220
    Processing helix  chain 'D' and resid 231 through 236
      removed outlier: 3.960A  pdb=" N   GLN D 236 " --> pdb=" O   GLU D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 241 through 259
      removed outlier: 4.176A  pdb=" N   ASP D 245 " --> pdb=" O   SER D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 309 through 320
      removed outlier: 3.955A  pdb=" N   GLU D 320 " --> pdb=" O   TYR D 316 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 331 through 342
      removed outlier: 3.597A  pdb=" N   GLN D 335 " --> pdb=" O   SER D 331 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 351 through 356
    Processing helix  chain 'D' and resid 358 through 367
      removed outlier: 3.518A  pdb=" N   LYS D 362 " --> pdb=" O   HIS D 358 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 370 through 380
    Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 354
      removed outlier: 5.971A  pdb=" N   LEU A 351 " --> pdb=" O   LYS A 367 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   LYS A 367 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   LEU A 417 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA A 418 " --> pdb=" O   MET A 412 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   GLN A 422 " --> pdb=" O   PHE A 408 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   PHE A 408 " --> pdb=" O   GLN A 422 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 426 through 428
      removed outlier: 4.211A  pdb=" N   SER A 427 " --> pdb=" O   LEU A 476 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 87
      removed outlier: 3.574A  pdb=" N   HIS B  87 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU B  92 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLY B 131 " --> pdb=" O   CYS B 142 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   GLU B 144 " --> pdb=" O   PHE B 129 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   PHE B 129 " --> pdb=" O   GLU B 144 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 196 through 198
    Processing sheet with id=AA5, first strand: chain 'C' and resid 365 through 367
      removed outlier: 6.498A  pdb=" N   GLN C 422 " --> pdb=" O   PHE C 408 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   PHE C 408 " --> pdb=" O   GLN C 422 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 474 through 477
    Processing sheet with id=AA7, first strand: chain 'D' and resid 72 through 73
      removed outlier: 3.673A  pdb=" N   ILE D  99 " --> pdb=" O   ILE D 139 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE D 139 " --> pdb=" O   ILE D  99 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLY D 131 " --> pdb=" O   CYS D 142 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   GLU D 144 " --> pdb=" O   PHE D 129 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   PHE D 129 " --> pdb=" O   GLU D 144 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 196 through 198

    395 hydrogen bonds defined for protein.
    1122 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: 1.33

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2427
        1.34 -     1.46: 1609
        1.46 -     1.58: 4721
        1.58 -     1.70: 3
        1.70 -     1.82: 101
  Bond restraints: 8861
  Sorted by residual:
  bond pdb=" N   PHE A 443 "
       pdb=" CA  PHE A 443 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.17e-02 7.31e+03 1.09e+01
  bond pdb=" N   VAL D 254 "
       pdb=" CA  VAL D 254 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.19e-02 7.06e+03 8.19e+00
  bond pdb=" N   VAL B 117 "
       pdb=" CA  VAL B 117 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.24e-02 6.50e+03 7.25e+00
  bond pdb=" C07 A1AHE D 401 "
       pdb=" N06 A1AHE D 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.442 -0.052 2.00e-02 2.50e+03 6.68e+00
  bond pdb=" N   GLN A 441 "
       pdb=" CA  GLN A 441 "
    ideal  model  delta    sigma   weight residual
    1.454  1.484 -0.030 1.16e-02 7.43e+03 6.65e+00
  ... (remaining 8856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 11477
        2.33 -     4.67: 381
        4.67 -     7.00: 68
        7.00 -     9.33: 24
        9.33 -    11.66: 2
  Bond angle restraints: 11952
  Sorted by residual:
  angle pdb=" CB  MET C 456 "
        pdb=" CG  MET C 456 "
        pdb=" SD  MET C 456 "
      ideal   model   delta    sigma   weight residual
     112.70  101.04   11.66 3.00e+00 1.11e-01 1.51e+01
  angle pdb=" CB  ARG C 583 "
        pdb=" CG  ARG C 583 "
        pdb=" CD  ARG C 583 "
      ideal   model   delta    sigma   weight residual
     111.30  120.03   -8.73 2.30e+00 1.89e-01 1.44e+01
  angle pdb=" C   PRO C 505 "
        pdb=" N   THR C 506 "
        pdb=" CA  THR C 506 "
      ideal   model   delta    sigma   weight residual
     121.54  128.56   -7.02 1.91e+00 2.74e-01 1.35e+01
  angle pdb=" CA  PHE A 443 "
        pdb=" CB  PHE A 443 "
        pdb=" CG  PHE A 443 "
      ideal   model   delta    sigma   weight residual
     113.80  117.39   -3.59 1.00e+00 1.00e+00 1.29e+01
  angle pdb=" C   TRP C 342 "
        pdb=" N   GLU C 343 "
        pdb=" CA  GLU C 343 "
      ideal   model   delta    sigma   weight residual
     121.54  128.26   -6.72 1.91e+00 2.74e-01 1.24e+01
  ... (remaining 11947 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4898
       17.96 -    35.91: 390
       35.91 -    53.87: 68
       53.87 -    71.83: 21
       71.83 -    89.78: 6
  Dihedral angle restraints: 5383
    sinusoidal: 2260
      harmonic: 3123
  Sorted by residual:
  dihedral pdb=" CA  MET D 146 "
           pdb=" C   MET D 146 "
           pdb=" N   ASP D 147 "
           pdb=" CA  ASP D 147 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.67  -34.33     0      5.00e+00 4.00e-02 4.71e+01
  dihedral pdb=" CA  GLN B 354 "
           pdb=" C   GLN B 354 "
           pdb=" N   LEU B 355 "
           pdb=" CA  LEU B 355 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.58   26.42     0      5.00e+00 4.00e-02 2.79e+01
  dihedral pdb=" CA  GLU D 114 "
           pdb=" C   GLU D 114 "
           pdb=" N   LEU D 115 "
           pdb=" CA  LEU D 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.00   26.00     0      5.00e+00 4.00e-02 2.70e+01
  ... (remaining 5380 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 767
       0.040 -    0.079: 335
       0.079 -    0.119: 146
       0.119 -    0.159: 49
       0.159 -    0.198: 17
  Chirality restraints: 1314
  Sorted by residual:
  chirality pdb=" CG  LEU D 314 "
            pdb=" CB  LEU D 314 "
            pdb=" CD1 LEU D 314 "
            pdb=" CD2 LEU D 314 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.83e-01
  chirality pdb=" CA  VAL D 254 "
            pdb=" N   VAL D 254 "
            pdb=" C   VAL D 254 "
            pdb=" CB  VAL D 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.93e-01
  chirality pdb=" CA  PHE C 599 "
            pdb=" N   PHE C 599 "
            pdb=" C   PHE C 599 "
            pdb=" CB  PHE C 599 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.64e-01
  ... (remaining 1311 not shown)

  Planarity restraints: 1511
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 554 "    0.501 9.50e-02 1.11e+02   2.26e-01 4.13e+01
        pdb=" NE  ARG C 554 "   -0.049 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 554 "    0.050 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 554 "   -0.021 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 554 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 381 "    0.046 5.00e-02 4.00e+02   7.08e-02 8.01e+00
        pdb=" N   PRO A 382 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 382 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 382 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 247 "   -0.018 2.00e-02 2.50e+03   1.50e-02 5.66e+00
        pdb=" CG  TRP B 247 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 247 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 247 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 247 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 247 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 247 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 247 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 247 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 247 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1508 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1572
        2.77 -     3.31: 8343
        3.31 -     3.84: 14200
        3.84 -     4.37: 16142
        4.37 -     4.90: 27342
  Nonbonded interactions: 67599
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 436 "
            pdb=" OG1 THR A 438 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OG  SER B 150 "
            pdb=" OE1 GLN B 153 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   LYS C 399 "
            pdb=" NZ  LYS C 462 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" O   ILE B 343 "
            pdb=" NH1 ARG B 349 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" NE2 GLN B 243 "
            pdb=" OD1 ASP B 351 "
     model   vdw
     2.328 3.120
  ... (remaining 67594 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 342 through 354 or resid 362 through 376 or resid 382 thro \ 
ugh 614))
  selection = (chain 'C' and (resid 342 through 354 or resid 362 through 494 or resid 500 thro \ 
ugh 614))
}
ncs_group {
  reference = (chain 'B' and (resid 59 through 72 or resid 81 through 401))
  selection = (chain 'D' and (resid 59 through 72 or resid 81 through 380 or resid 401))
}

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:             0.520
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.320
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
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      :  0.005   0.052   8861  Z= 0.246
  Angle     :  1.004  11.665  11952  Z= 0.510
  Chirality :  0.057   0.198   1314
  Planarity :  0.009   0.226   1511
  Dihedral  : 13.776  89.785   3363
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.17 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.47 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.06 (0.24), residues: 1055
  helix: -0.55 (0.23), residues: 445
  sheet:  0.47 (0.64), residues: 70
  loop : -0.92 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.056   0.002   ARG C 554 
 TYR   0.022   0.002   TYR B 229 
 PHE   0.040   0.003   PHE D 337 
 TRP   0.040   0.002   TRP B 247 
 HIS   0.013   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 8861)
  covalent geometry    : angle       1.00421 (11952)
  hydrogen bonds       : bond        0.18013 (  395)
  hydrogen bonds       : angle       7.70375 ( 1122)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 236
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 PHE cc_start: 0.8465 (m-10) cc_final: 0.8157 (m-80)
REVERT: A  391 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8451 (mmm-85)
REVERT: A  409 MET cc_start: 0.9261 (mtt) cc_final: 0.8769 (mpp)
REVERT: A  447 ASP cc_start: 0.8951 (m-30) cc_final: 0.8629 (m-30)
REVERT: A  486 ASP cc_start: 0.8372 (t0) cc_final: 0.8114 (t70)
REVERT: A  552 ASN cc_start: 0.7581 (p0) cc_final: 0.7178 (p0)
REVERT: B  197 LEU cc_start: 0.8484 (mm) cc_final: 0.8282 (mm)
REVERT: C  393 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7379 (mt-10)
REVERT: C  456 MET cc_start: 0.9305 (mmt) cc_final: 0.9080 (mmm)
REVERT: C  537 VAL cc_start: 0.9143 (t) cc_final: 0.8940 (t)
REVERT: C  598 LEU cc_start: 0.8548 (mt) cc_final: 0.8253 (mt)
REVERT: D   94 MET cc_start: 0.8599 (mpp) cc_final: 0.8153 (mpp)
REVERT: D  199 ASN cc_start: 0.8830 (t0) cc_final: 0.8482 (t0)
REVERT: D  209 PHE cc_start: 0.8645 (p90) cc_final: 0.8327 (p90)
REVERT: D  240 TYR cc_start: 0.7501 (p90) cc_final: 0.6932 (p90)
REVERT: D  317 ILE cc_start: 0.9375 (mm) cc_final: 0.9163 (mm)
REVERT: D  343 ILE cc_start: 0.7782 (mt) cc_final: 0.7482 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 236
  average time/residue: 0.0937
  time to fit residues: 30.8636
Evaluate side-chains
  183 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0980
   overall best weight:    1.6186

-------------------------------------------------------------------------------
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 = 0.3608 r_free = 0.3608 target = 0.101815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.080973 restraints weight = 26001.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.083358 restraints weight = 15118.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.085020 restraints weight = 10479.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.086187 restraints weight = 8119.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.086943 restraints weight = 6802.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8861  Z= 0.152
  Angle     :  0.602   6.657  11952  Z= 0.315
  Chirality :  0.045   0.152   1314
  Planarity :  0.005   0.042   1511
  Dihedral  :  5.009  29.299   1210
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.22 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.88 %
    Favored  : 95.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.14 (0.25), residues: 1055
  helix:  0.51 (0.24), residues: 469
  sheet:  0.41 (0.57), residues: 89
  loop : -0.70 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 363 
 TYR   0.012   0.002   TYR D 134 
 PHE   0.012   0.002   PHE D 337 
 TRP   0.016   0.002   TRP B 247 
 HIS   0.011   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8861)
  covalent geometry    : angle       0.60236 (11952)
  hydrogen bonds       : bond        0.03622 (  395)
  hydrogen bonds       : angle       5.23108 ( 1122)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 244
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 MET cc_start: 0.7715 (mmm) cc_final: 0.7296 (mmm)
REVERT: A  436 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7800 (tm-30)
REVERT: A  486 ASP cc_start: 0.8565 (t0) cc_final: 0.8101 (t0)
REVERT: A  523 ASN cc_start: 0.8039 (t0) cc_final: 0.7780 (p0)
REVERT: A  532 TYR cc_start: 0.8039 (t80) cc_final: 0.7768 (t80)
REVERT: A  552 ASN cc_start: 0.7913 (p0) cc_final: 0.7686 (p0)
REVERT: B  110 GLN cc_start: 0.9460 (mt0) cc_final: 0.9256 (mt0)
REVERT: B  182 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8299 (mm-30)
REVERT: B  253 LEU cc_start: 0.9256 (mm) cc_final: 0.8903 (mm)
REVERT: B  314 LEU cc_start: 0.9054 (mt) cc_final: 0.8826 (mt)
REVERT: B  324 LYS cc_start: 0.8005 (pttt) cc_final: 0.7319 (mmtt)
REVERT: C  393 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7354 (mt-10)
REVERT: C  401 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7860 (mtp85)
REVERT: C  442 MET cc_start: 0.8677 (mmp) cc_final: 0.8407 (mtt)
REVERT: C  444 GLN cc_start: 0.8813 (mt0) cc_final: 0.8487 (mt0)
REVERT: C  458 TYR cc_start: 0.9008 (t80) cc_final: 0.8160 (t80)
REVERT: C  469 MET cc_start: 0.9240 (mmp) cc_final: 0.8836 (tpp)
REVERT: C  583 ARG cc_start: 0.8472 (tpm170) cc_final: 0.8169 (tpm170)
REVERT: D   94 MET cc_start: 0.8004 (mpp) cc_final: 0.7425 (mpp)
REVERT: D  199 ASN cc_start: 0.8532 (t0) cc_final: 0.8025 (t0)
REVERT: D  209 PHE cc_start: 0.8973 (p90) cc_final: 0.8670 (p90)
REVERT: D  240 TYR cc_start: 0.7517 (p90) cc_final: 0.6981 (p90)
REVERT: D  317 ILE cc_start: 0.9385 (mm) cc_final: 0.9170 (mm)
REVERT: D  343 ILE cc_start: 0.7925 (mt) cc_final: 0.7484 (mt)
  outliers start: 3
  outliers final: 0
  residues processed: 244
  average time/residue: 0.0910
  time to fit residues: 31.2752
Evaluate side-chains
  191 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 92 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 15 optimal weight:    0.3980
   chunk 18 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 3 optimal weight:    9.9990
   chunk 56 optimal weight:    0.5980
   chunk 13 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3639 r_free = 0.3639 target = 0.103903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.082914 restraints weight = 25778.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.085503 restraints weight = 14919.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.087221 restraints weight = 10235.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.088484 restraints weight = 7920.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.089102 restraints weight = 6552.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8861  Z= 0.102
  Angle     :  0.543   5.422  11952  Z= 0.283
  Chirality :  0.044   0.130   1314
  Planarity :  0.004   0.039   1511
  Dihedral  :  4.609  28.099   1210
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.51 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.26), residues: 1055
  helix:  1.01 (0.24), residues: 467
  sheet:  0.47 (0.60), residues: 79
  loop : -0.58 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 363 
 TYR   0.017   0.001   TYR C 534 
 PHE   0.044   0.001   PHE A 387 
 TRP   0.016   0.001   TRP D 247 
 HIS   0.008   0.001   HIS D 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 8861)
  covalent geometry    : angle       0.54252 (11952)
  hydrogen bonds       : bond        0.03285 (  395)
  hydrogen bonds       : angle       4.92640 ( 1122)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 MET cc_start: 0.7720 (mmm) cc_final: 0.7231 (mmm)
REVERT: A  436 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7694 (tm-30)
REVERT: A  473 ASN cc_start: 0.8569 (m110) cc_final: 0.8025 (m-40)
REVERT: A  486 ASP cc_start: 0.8483 (t0) cc_final: 0.7969 (t0)
REVERT: A  523 ASN cc_start: 0.8087 (t0) cc_final: 0.7796 (p0)
REVERT: A  552 ASN cc_start: 0.7952 (p0) cc_final: 0.7659 (p0)
REVERT: B  110 GLN cc_start: 0.9456 (mt0) cc_final: 0.9239 (mt0)
REVERT: B  182 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8292 (mm-30)
REVERT: B  197 LEU cc_start: 0.8531 (mm) cc_final: 0.8300 (mm)
REVERT: B  253 LEU cc_start: 0.9260 (mm) cc_final: 0.8968 (mm)
REVERT: B  314 LEU cc_start: 0.9157 (mt) cc_final: 0.8854 (mt)
REVERT: B  324 LYS cc_start: 0.7972 (pttt) cc_final: 0.7247 (mmtt)
REVERT: C  412 MET cc_start: 0.6753 (ttt) cc_final: 0.6537 (ttt)
REVERT: C  442 MET cc_start: 0.8751 (mmp) cc_final: 0.8315 (ttt)
REVERT: C  444 GLN cc_start: 0.8824 (mt0) cc_final: 0.8443 (mt0)
REVERT: C  458 TYR cc_start: 0.8963 (t80) cc_final: 0.8201 (t80)
REVERT: C  469 MET cc_start: 0.9154 (mmp) cc_final: 0.8949 (tpp)
REVERT: C  521 ASP cc_start: 0.6882 (t70) cc_final: 0.6481 (t70)
REVERT: C  553 ASN cc_start: 0.8704 (t0) cc_final: 0.8296 (t0)
REVERT: C  583 ARG cc_start: 0.8439 (tpm170) cc_final: 0.8198 (tpm170)
REVERT: D   94 MET cc_start: 0.8240 (mpp) cc_final: 0.7896 (mpp)
REVERT: D  199 ASN cc_start: 0.8792 (t0) cc_final: 0.8568 (t0)
REVERT: D  209 PHE cc_start: 0.8953 (p90) cc_final: 0.8703 (p90)
REVERT: D  240 TYR cc_start: 0.7631 (p90) cc_final: 0.6903 (p90)
REVERT: D  317 ILE cc_start: 0.9376 (mm) cc_final: 0.9122 (mm)
REVERT: D  324 LYS cc_start: 0.6677 (mmtt) cc_final: 0.6400 (mmtt)
REVERT: D  343 ILE cc_start: 0.7872 (mt) cc_final: 0.7187 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 252
  average time/residue: 0.0868
  time to fit residues: 30.9532
Evaluate side-chains
  194 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 40 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0000
   chunk 62 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.5190

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.100710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.080312 restraints weight = 26152.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.082817 restraints weight = 14884.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.084519 restraints weight = 10119.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.085417 restraints weight = 7757.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.086383 restraints weight = 6617.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8861  Z= 0.138
  Angle     :  0.562   5.651  11952  Z= 0.296
  Chirality :  0.045   0.159   1314
  Planarity :  0.004   0.037   1511
  Dihedral  :  4.698  29.580   1210
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.22 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.26), residues: 1055
  helix:  1.15 (0.24), residues: 467
  sheet:  0.07 (0.67), residues: 61
  loop : -0.51 (0.27), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 189 
 TYR   0.015   0.001   TYR D 134 
 PHE   0.015   0.001   PHE A 387 
 TRP   0.019   0.002   TRP D 247 
 HIS   0.006   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 8861)
  covalent geometry    : angle       0.56172 (11952)
  hydrogen bonds       : bond        0.03222 (  395)
  hydrogen bonds       : angle       4.86586 ( 1122)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 MET cc_start: 0.7748 (mmm) cc_final: 0.7091 (mmm)
REVERT: A  417 LEU cc_start: 0.8879 (mt) cc_final: 0.8373 (pt)
REVERT: A  436 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: A  441 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8609 (tm-30)
REVERT: A  480 LEU cc_start: 0.9188 (tt) cc_final: 0.8963 (tp)
REVERT: A  486 ASP cc_start: 0.8559 (t0) cc_final: 0.7963 (t0)
REVERT: A  523 ASN cc_start: 0.8221 (t0) cc_final: 0.7882 (p0)
REVERT: A  532 TYR cc_start: 0.8654 (t80) cc_final: 0.8444 (t80)
REVERT: A  552 ASN cc_start: 0.7916 (p0) cc_final: 0.7646 (p0)
REVERT: A  553 ASN cc_start: 0.9218 (t0) cc_final: 0.8838 (t0)
REVERT: B  110 GLN cc_start: 0.9477 (mt0) cc_final: 0.9253 (mt0)
REVERT: B  143 MET cc_start: 0.7864 (ptp) cc_final: 0.7633 (ptp)
REVERT: B  182 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8329 (mm-30)
REVERT: B  190 ASP cc_start: 0.8288 (t0) cc_final: 0.7897 (t0)
REVERT: B  197 LEU cc_start: 0.8582 (mm) cc_final: 0.8380 (mm)
REVERT: B  253 LEU cc_start: 0.9211 (mm) cc_final: 0.8991 (mm)
REVERT: B  324 LYS cc_start: 0.7574 (pttt) cc_final: 0.6924 (mmtt)
REVERT: C  385 GLU cc_start: 0.8268 (pm20) cc_final: 0.7547 (pm20)
REVERT: C  444 GLN cc_start: 0.8749 (mt0) cc_final: 0.8377 (mt0)
REVERT: C  458 TYR cc_start: 0.9004 (t80) cc_final: 0.8254 (t80)
REVERT: C  521 ASP cc_start: 0.7162 (t70) cc_final: 0.6776 (t70)
REVERT: C  583 ARG cc_start: 0.8421 (tpm170) cc_final: 0.8155 (tpm170)
REVERT: D   94 MET cc_start: 0.8197 (mpp) cc_final: 0.7831 (mpp)
REVERT: D  199 ASN cc_start: 0.9146 (t0) cc_final: 0.8729 (t0)
REVERT: D  209 PHE cc_start: 0.9015 (p90) cc_final: 0.8662 (p90)
REVERT: D  249 MET cc_start: 0.8625 (ppp) cc_final: 0.8409 (ppp)
REVERT: D  317 ILE cc_start: 0.9340 (mm) cc_final: 0.9091 (mt)
REVERT: D  324 LYS cc_start: 0.6751 (mmtt) cc_final: 0.6397 (mmmt)
REVERT: D  343 ILE cc_start: 0.7909 (mt) cc_final: 0.7331 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.0840
  time to fit residues: 28.7364
Evaluate side-chains
  196 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    7.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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 = 0.3532 r_free = 0.3532 target = 0.097322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.076616 restraints weight = 26772.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.079148 restraints weight = 15095.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.080850 restraints weight = 10207.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.082060 restraints weight = 7812.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.082752 restraints weight = 6476.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.3292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8861  Z= 0.195
  Angle     :  0.639   7.357  11952  Z= 0.333
  Chirality :  0.047   0.217   1314
  Planarity :  0.004   0.035   1511
  Dihedral  :  5.120  31.615   1210
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  3.89 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.26), residues: 1055
  helix:  0.95 (0.24), residues: 469
  sheet:  0.00 (0.66), residues: 55
  loop : -0.53 (0.27), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 401 
 TYR   0.016   0.002   TYR D 134 
 PHE   0.024   0.002   PHE B 133 
 TRP   0.023   0.002   TRP B 247 
 HIS   0.007   0.002   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 8861)
  covalent geometry    : angle       0.63929 (11952)
  hydrogen bonds       : bond        0.03741 (  395)
  hydrogen bonds       : angle       5.14339 ( 1122)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 MET cc_start: 0.8004 (mmm) cc_final: 0.7103 (mmm)
REVERT: A  417 LEU cc_start: 0.8946 (mt) cc_final: 0.8504 (pt)
REVERT: A  436 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7833 (tm-30)
REVERT: A  447 ASP cc_start: 0.9059 (m-30) cc_final: 0.8840 (m-30)
REVERT: A  486 ASP cc_start: 0.8452 (t0) cc_final: 0.7947 (t0)
REVERT: A  504 GLN cc_start: 0.8173 (mm110) cc_final: 0.7188 (pm20)
REVERT: A  532 TYR cc_start: 0.8763 (t80) cc_final: 0.8407 (t80)
REVERT: A  552 ASN cc_start: 0.7906 (p0) cc_final: 0.7658 (p0)
REVERT: A  553 ASN cc_start: 0.9179 (t0) cc_final: 0.8734 (t0)
REVERT: B  110 GLN cc_start: 0.9485 (mt0) cc_final: 0.9163 (mt0)
REVERT: B  182 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8469 (mm-30)
REVERT: B  190 ASP cc_start: 0.8505 (t0) cc_final: 0.7737 (t0)
REVERT: B  224 VAL cc_start: 0.7921 (m) cc_final: 0.7622 (p)
REVERT: B  253 LEU cc_start: 0.9231 (mm) cc_final: 0.8771 (mm)
REVERT: B  314 LEU cc_start: 0.9114 (mt) cc_final: 0.8903 (mt)
REVERT: B  324 LYS cc_start: 0.7589 (pttt) cc_final: 0.6977 (mmtt)
REVERT: C  412 MET cc_start: 0.6548 (ttt) cc_final: 0.6238 (tmm)
REVERT: C  444 GLN cc_start: 0.8862 (mt0) cc_final: 0.8443 (mt0)
REVERT: C  458 TYR cc_start: 0.8931 (t80) cc_final: 0.8708 (t80)
REVERT: C  521 ASP cc_start: 0.7157 (t70) cc_final: 0.6801 (t70)
REVERT: C  553 ASN cc_start: 0.8567 (t0) cc_final: 0.8251 (t0)
REVERT: D   94 MET cc_start: 0.8274 (mpp) cc_final: 0.7914 (mpp)
REVERT: D  199 ASN cc_start: 0.8987 (t0) cc_final: 0.8387 (t0)
REVERT: D  209 PHE cc_start: 0.9141 (p90) cc_final: 0.8588 (p90)
REVERT: D  249 MET cc_start: 0.8851 (ppp) cc_final: 0.8628 (ppp)
REVERT: D  310 ILE cc_start: 0.8104 (tp) cc_final: 0.7628 (tt)
REVERT: D  317 ILE cc_start: 0.9323 (mm) cc_final: 0.9068 (mt)
REVERT: D  343 ILE cc_start: 0.8294 (mt) cc_final: 0.7908 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.0782
  time to fit residues: 27.4473
Evaluate side-chains
  179 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 34 optimal weight:    9.9990
   chunk 103 optimal weight:    0.9990
   chunk 27 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0000
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.7588

-------------------------------------------------------------------------------
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 = 0.3571 r_free = 0.3571 target = 0.099792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.078762 restraints weight = 26199.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.081307 restraints weight = 14845.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.083029 restraints weight = 10100.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.084240 restraints weight = 7744.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.085001 restraints weight = 6428.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.3357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8861  Z= 0.107
  Angle     :  0.568   7.062  11952  Z= 0.296
  Chirality :  0.045   0.167   1314
  Planarity :  0.003   0.035   1511
  Dihedral  :  4.743  30.911   1210
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.32 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.26), residues: 1055
  helix:  1.17 (0.24), residues: 474
  sheet:  0.10 (0.63), residues: 65
  loop : -0.43 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 401 
 TYR   0.025   0.001   TYR C 534 
 PHE   0.014   0.001   PHE A 387 
 TRP   0.016   0.001   TRP B 247 
 HIS   0.005   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 8861)
  covalent geometry    : angle       0.56782 (11952)
  hydrogen bonds       : bond        0.03133 (  395)
  hydrogen bonds       : angle       4.77288 ( 1122)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 257
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 PHE cc_start: 0.8284 (m-80) cc_final: 0.7635 (m-80)
REVERT: A  412 MET cc_start: 0.8168 (mmm) cc_final: 0.7632 (mmt)
REVERT: A  417 LEU cc_start: 0.9117 (mt) cc_final: 0.8915 (mt)
REVERT: A  436 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7747 (tm-30)
REVERT: A  486 ASP cc_start: 0.8339 (t0) cc_final: 0.7576 (t0)
REVERT: A  504 GLN cc_start: 0.8100 (mm110) cc_final: 0.7146 (pm20)
REVERT: A  512 MET cc_start: 0.8601 (mtt) cc_final: 0.8400 (mtt)
REVERT: A  552 ASN cc_start: 0.7881 (p0) cc_final: 0.7630 (p0)
REVERT: A  553 ASN cc_start: 0.9197 (t0) cc_final: 0.8747 (t0)
REVERT: A  581 MET cc_start: 0.8467 (tpt) cc_final: 0.7766 (tpp)
REVERT: B  110 GLN cc_start: 0.9465 (mt0) cc_final: 0.8966 (mt0)
REVERT: B  182 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8731 (mm-30)
REVERT: B  188 HIS cc_start: 0.8315 (t70) cc_final: 0.8110 (t-90)
REVERT: B  190 ASP cc_start: 0.8437 (t0) cc_final: 0.7658 (t0)
REVERT: B  197 LEU cc_start: 0.8692 (mm) cc_final: 0.8461 (mm)
REVERT: B  224 VAL cc_start: 0.8182 (m) cc_final: 0.7905 (p)
REVERT: B  314 LEU cc_start: 0.9039 (mt) cc_final: 0.8836 (mt)
REVERT: B  324 LYS cc_start: 0.7564 (pttt) cc_final: 0.6991 (mmtt)
REVERT: C  412 MET cc_start: 0.6348 (ttt) cc_final: 0.5189 (tmm)
REVERT: C  442 MET cc_start: 0.8831 (mmp) cc_final: 0.7998 (mtp)
REVERT: C  444 GLN cc_start: 0.8825 (mt0) cc_final: 0.8394 (mt0)
REVERT: C  458 TYR cc_start: 0.8946 (t80) cc_final: 0.8406 (t80)
REVERT: C  468 ASP cc_start: 0.9117 (t0) cc_final: 0.8749 (t0)
REVERT: C  493 LYS cc_start: 0.9226 (tppt) cc_final: 0.8760 (tptt)
REVERT: C  521 ASP cc_start: 0.7142 (t70) cc_final: 0.6799 (t70)
REVERT: C  553 ASN cc_start: 0.8558 (t0) cc_final: 0.8230 (t0)
REVERT: D   94 MET cc_start: 0.8220 (mpp) cc_final: 0.7825 (mpp)
REVERT: D  209 PHE cc_start: 0.9023 (p90) cc_final: 0.8586 (p90)
REVERT: D  249 MET cc_start: 0.8863 (ppp) cc_final: 0.8587 (ppp)
REVERT: D  310 ILE cc_start: 0.7874 (tp) cc_final: 0.7250 (tt)
REVERT: D  317 ILE cc_start: 0.9293 (mm) cc_final: 0.9029 (mt)
REVERT: D  343 ILE cc_start: 0.8153 (mt) cc_final: 0.7653 (mt)
REVERT: D  378 THR cc_start: 0.7887 (m) cc_final: 0.6440 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 257
  average time/residue: 0.0779
  time to fit residues: 29.3677
Evaluate side-chains
  188 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 101 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3541 r_free = 0.3541 target = 0.097652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.077254 restraints weight = 26738.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.079706 restraints weight = 15375.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.081391 restraints weight = 10527.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.082421 restraints weight = 8081.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.083208 restraints weight = 6807.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8861  Z= 0.159
  Angle     :  0.626   7.055  11952  Z= 0.328
  Chirality :  0.047   0.208   1314
  Planarity :  0.004   0.045   1511
  Dihedral  :  4.999  31.955   1210
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.70 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.26), residues: 1055
  helix:  0.94 (0.24), residues: 474
  sheet:  0.09 (0.59), residues: 75
  loop : -0.49 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 563 
 TYR   0.023   0.002   TYR C 534 
 PHE   0.023   0.002   PHE A 390 
 TRP   0.020   0.002   TRP B 247 
 HIS   0.018   0.002   HIS C 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 8861)
  covalent geometry    : angle       0.62647 (11952)
  hydrogen bonds       : bond        0.03387 (  395)
  hydrogen bonds       : angle       5.03864 ( 1122)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 MET cc_start: 0.8472 (mmm) cc_final: 0.7349 (mmm)
REVERT: A  436 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7888 (tm-30)
REVERT: A  486 ASP cc_start: 0.8311 (t0) cc_final: 0.7241 (t0)
REVERT: A  504 GLN cc_start: 0.8181 (mm110) cc_final: 0.7125 (pp30)
REVERT: A  553 ASN cc_start: 0.9211 (t0) cc_final: 0.8886 (t0)
REVERT: B  110 GLN cc_start: 0.9446 (mt0) cc_final: 0.8978 (mt0)
REVERT: B  182 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8713 (mm-30)
REVERT: B  190 ASP cc_start: 0.8414 (t0) cc_final: 0.7610 (t0)
REVERT: B  197 LEU cc_start: 0.8471 (mm) cc_final: 0.8261 (mm)
REVERT: B  314 LEU cc_start: 0.9081 (mt) cc_final: 0.8866 (mt)
REVERT: B  324 LYS cc_start: 0.7618 (pttt) cc_final: 0.6941 (mmtt)
REVERT: C  412 MET cc_start: 0.6097 (ttt) cc_final: 0.5370 (tmm)
REVERT: C  416 ASN cc_start: 0.8784 (p0) cc_final: 0.8230 (p0)
REVERT: C  444 GLN cc_start: 0.8780 (mt0) cc_final: 0.8445 (mt0)
REVERT: C  493 LYS cc_start: 0.9067 (tppt) cc_final: 0.8733 (tptt)
REVERT: C  521 ASP cc_start: 0.7237 (t70) cc_final: 0.6947 (t70)
REVERT: C  522 ASN cc_start: 0.7634 (t0) cc_final: 0.7174 (t0)
REVERT: C  553 ASN cc_start: 0.8724 (t0) cc_final: 0.8347 (t0)
REVERT: C  577 CYS cc_start: 0.7861 (m) cc_final: 0.7522 (t)
REVERT: D   94 MET cc_start: 0.8207 (mpp) cc_final: 0.7908 (mpp)
REVERT: D  199 ASN cc_start: 0.9088 (t0) cc_final: 0.8833 (t0)
REVERT: D  209 PHE cc_start: 0.9124 (p90) cc_final: 0.8684 (p90)
REVERT: D  249 MET cc_start: 0.8846 (ppp) cc_final: 0.8624 (ppp)
REVERT: D  317 ILE cc_start: 0.9273 (mm) cc_final: 0.9055 (mt)
REVERT: D  343 ILE cc_start: 0.8278 (mt) cc_final: 0.7814 (mt)
REVERT: D  378 THR cc_start: 0.7907 (m) cc_final: 0.7334 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.0736
  time to fit residues: 25.2787
Evaluate side-chains
  181 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 78 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 80 optimal weight:    9.9990
   chunk 103 optimal weight:    8.9990
   chunk 96 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 102 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   overall best weight:    2.3586

-------------------------------------------------------------------------------
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 = 0.3510 r_free = 0.3510 target = 0.095828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.075765 restraints weight = 26508.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.078138 restraints weight = 15036.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.079734 restraints weight = 10207.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.080827 restraints weight = 7805.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.081486 restraints weight = 6509.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.4014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8861  Z= 0.194
  Angle     :  0.666   7.836  11952  Z= 0.346
  Chirality :  0.047   0.193   1314
  Planarity :  0.004   0.033   1511
  Dihedral  :  5.243  32.704   1210
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.79 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.26), residues: 1055
  helix:  0.83 (0.24), residues: 473
  sheet: -0.16 (0.59), residues: 73
  loop : -0.58 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 563 
 TYR   0.021   0.002   TYR D 134 
 PHE   0.014   0.002   PHE A 443 
 TRP   0.026   0.002   TRP B 247 
 HIS   0.005   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 8861)
  covalent geometry    : angle       0.66626 (11952)
  hydrogen bonds       : bond        0.03699 (  395)
  hydrogen bonds       : angle       5.19997 ( 1122)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 PHE cc_start: 0.8121 (m-80) cc_final: 0.7649 (m-80)
REVERT: A  412 MET cc_start: 0.8495 (mmm) cc_final: 0.7725 (mmt)
REVERT: A  417 LEU cc_start: 0.8915 (mt) cc_final: 0.8419 (pt)
REVERT: A  436 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7905 (tm-30)
REVERT: A  456 MET cc_start: 0.9317 (mmm) cc_final: 0.9032 (mmt)
REVERT: A  486 ASP cc_start: 0.8139 (t0) cc_final: 0.7369 (t0)
REVERT: A  504 GLN cc_start: 0.8142 (mm110) cc_final: 0.7009 (pp30)
REVERT: A  532 TYR cc_start: 0.8718 (t80) cc_final: 0.8465 (t80)
REVERT: A  553 ASN cc_start: 0.9241 (t0) cc_final: 0.8908 (t0)
REVERT: B   68 PHE cc_start: 0.8623 (m-80) cc_final: 0.8358 (m-10)
REVERT: B  110 GLN cc_start: 0.9489 (mt0) cc_final: 0.8995 (mt0)
REVERT: B  182 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8738 (mm-30)
REVERT: B  190 ASP cc_start: 0.8496 (t0) cc_final: 0.7842 (t0)
REVERT: B  192 LYS cc_start: 0.9250 (pttt) cc_final: 0.8924 (ptmm)
REVERT: B  197 LEU cc_start: 0.8685 (mm) cc_final: 0.8455 (mm)
REVERT: B  229 TYR cc_start: 0.8843 (m-80) cc_final: 0.8613 (m-80)
REVERT: B  324 LYS cc_start: 0.8135 (pttt) cc_final: 0.7145 (mmtt)
REVERT: C  412 MET cc_start: 0.6378 (ttt) cc_final: 0.5561 (tmm)
REVERT: C  442 MET cc_start: 0.8683 (mmp) cc_final: 0.7944 (mtp)
REVERT: C  444 GLN cc_start: 0.8828 (mt0) cc_final: 0.8453 (mt0)
REVERT: C  458 TYR cc_start: 0.8924 (t80) cc_final: 0.8491 (t80)
REVERT: C  583 ARG cc_start: 0.8480 (tpp-160) cc_final: 0.8047 (tpm170)
REVERT: D  199 ASN cc_start: 0.9134 (t0) cc_final: 0.8887 (t0)
REVERT: D  209 PHE cc_start: 0.9185 (p90) cc_final: 0.8640 (p90)
REVERT: D  314 LEU cc_start: 0.8642 (mp) cc_final: 0.8428 (mp)
REVERT: D  317 ILE cc_start: 0.9453 (mm) cc_final: 0.9213 (mt)
REVERT: D  343 ILE cc_start: 0.8466 (mt) cc_final: 0.8095 (mt)
REVERT: D  378 THR cc_start: 0.7892 (m) cc_final: 0.7495 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.0753
  time to fit residues: 23.3915
Evaluate side-chains
  175 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 81 optimal weight:    7.9990
   chunk 60 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.097164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.076792 restraints weight = 26568.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.079215 restraints weight = 15111.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.080897 restraints weight = 10289.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.082021 restraints weight = 7876.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.082742 restraints weight = 6560.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.4142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8861  Z= 0.155
  Angle     :  0.656   9.578  11952  Z= 0.339
  Chirality :  0.048   0.202   1314
  Planarity :  0.004   0.033   1511
  Dihedral  :  5.109  32.289   1210
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.17 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.26), residues: 1055
  helix:  0.81 (0.24), residues: 476
  sheet: -0.40 (0.56), residues: 82
  loop : -0.47 (0.29), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 563 
 TYR   0.020   0.002   TYR C 534 
 PHE   0.024   0.002   PHE A 390 
 TRP   0.020   0.002   TRP B 247 
 HIS   0.005   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 8861)
  covalent geometry    : angle       0.65637 (11952)
  hydrogen bonds       : bond        0.03485 (  395)
  hydrogen bonds       : angle       5.08250 ( 1122)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 MET cc_start: 0.8499 (mmm) cc_final: 0.7766 (mmt)
REVERT: A  436 GLN cc_start: 0.8366 (tm-30) cc_final: 0.7872 (tm-30)
REVERT: A  441 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8137 (tm-30)
REVERT: A  456 MET cc_start: 0.9337 (mmm) cc_final: 0.9042 (mmt)
REVERT: A  486 ASP cc_start: 0.8503 (t0) cc_final: 0.7733 (t0)
REVERT: A  504 GLN cc_start: 0.8118 (mm110) cc_final: 0.6990 (pm20)
REVERT: A  532 TYR cc_start: 0.8625 (t80) cc_final: 0.8331 (t80)
REVERT: A  553 ASN cc_start: 0.9198 (t0) cc_final: 0.8915 (t0)
REVERT: B  110 GLN cc_start: 0.9485 (mt0) cc_final: 0.9049 (mt0)
REVERT: B  115 LEU cc_start: 0.9612 (mt) cc_final: 0.9402 (mt)
REVERT: B  182 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8762 (mm-30)
REVERT: B  190 ASP cc_start: 0.8469 (t0) cc_final: 0.7774 (t0)
REVERT: B  197 LEU cc_start: 0.8619 (mm) cc_final: 0.8397 (mm)
REVERT: B  229 TYR cc_start: 0.8749 (m-80) cc_final: 0.8426 (m-80)
REVERT: B  314 LEU cc_start: 0.9071 (mt) cc_final: 0.8855 (mt)
REVERT: B  324 LYS cc_start: 0.8217 (pttt) cc_final: 0.7193 (mmtt)
REVERT: C  412 MET cc_start: 0.6383 (ttt) cc_final: 0.5567 (tmm)
REVERT: C  416 ASN cc_start: 0.8729 (p0) cc_final: 0.8052 (p0)
REVERT: C  442 MET cc_start: 0.8723 (mmp) cc_final: 0.7988 (mtp)
REVERT: C  444 GLN cc_start: 0.8825 (mt0) cc_final: 0.8439 (mt0)
REVERT: C  458 TYR cc_start: 0.8907 (t80) cc_final: 0.8485 (t80)
REVERT: C  521 ASP cc_start: 0.7652 (t70) cc_final: 0.7321 (t70)
REVERT: C  553 ASN cc_start: 0.8683 (t0) cc_final: 0.8344 (t0)
REVERT: D   94 MET cc_start: 0.8043 (mpp) cc_final: 0.7643 (mpp)
REVERT: D  199 ASN cc_start: 0.9054 (t0) cc_final: 0.8838 (t0)
REVERT: D  209 PHE cc_start: 0.9184 (p90) cc_final: 0.8665 (p90)
REVERT: D  249 MET cc_start: 0.8487 (ppp) cc_final: 0.8139 (ppp)
REVERT: D  317 ILE cc_start: 0.9455 (mm) cc_final: 0.9212 (mt)
REVERT: D  343 ILE cc_start: 0.8415 (mt) cc_final: 0.8052 (mt)
REVERT: D  378 THR cc_start: 0.7933 (m) cc_final: 0.7495 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.0698
  time to fit residues: 23.7500
Evaluate side-chains
  183 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0020
   chunk 24 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 18 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.6790

-------------------------------------------------------------------------------
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 = 0.3583 r_free = 0.3583 target = 0.099245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.078856 restraints weight = 26184.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.081303 restraints weight = 14846.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.083043 restraints weight = 10100.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.084100 restraints weight = 7718.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.084951 restraints weight = 6481.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.4133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8861  Z= 0.113
  Angle     :  0.637   8.432  11952  Z= 0.327
  Chirality :  0.047   0.200   1314
  Planarity :  0.004   0.034   1511
  Dihedral  :  4.840  30.893   1210
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.79 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.26), residues: 1055
  helix:  0.95 (0.24), residues: 478
  sheet: -0.29 (0.54), residues: 93
  loop : -0.34 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 563 
 TYR   0.029   0.001   TYR C 534 
 PHE   0.020   0.001   PHE A 390 
 TRP   0.019   0.001   TRP B 247 
 HIS   0.004   0.001   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8861)
  covalent geometry    : angle       0.63669 (11952)
  hydrogen bonds       : bond        0.03261 (  395)
  hydrogen bonds       : angle       4.90768 ( 1122)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 MET cc_start: 0.8532 (mmm) cc_final: 0.7839 (mmt)
REVERT: A  436 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7807 (tm-30)
REVERT: A  441 GLN cc_start: 0.9087 (tm-30) cc_final: 0.8377 (tm-30)
REVERT: A  456 MET cc_start: 0.9322 (mmm) cc_final: 0.8969 (mmt)
REVERT: A  486 ASP cc_start: 0.8465 (t0) cc_final: 0.7275 (t0)
REVERT: A  517 ILE cc_start: 0.8747 (mt) cc_final: 0.8146 (mt)
REVERT: A  521 ASP cc_start: 0.8387 (t0) cc_final: 0.6701 (p0)
REVERT: A  553 ASN cc_start: 0.9179 (t0) cc_final: 0.8925 (t0)
REVERT: B   68 PHE cc_start: 0.8353 (m-10) cc_final: 0.7694 (m-80)
REVERT: B  110 GLN cc_start: 0.9452 (mt0) cc_final: 0.9027 (mt0)
REVERT: B  111 ILE cc_start: 0.9239 (mt) cc_final: 0.8967 (mt)
REVERT: B  115 LEU cc_start: 0.9412 (mt) cc_final: 0.9210 (mt)
REVERT: B  141 ILE cc_start: 0.9379 (mp) cc_final: 0.9072 (tp)
REVERT: B  182 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8677 (mm-30)
REVERT: B  183 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8459 (ttmt)
REVERT: B  190 ASP cc_start: 0.8341 (t0) cc_final: 0.7727 (t0)
REVERT: B  197 LEU cc_start: 0.8468 (mm) cc_final: 0.8189 (mm)
REVERT: B  229 TYR cc_start: 0.8612 (m-80) cc_final: 0.8340 (m-80)
REVERT: B  324 LYS cc_start: 0.8182 (pttt) cc_final: 0.7222 (mmtt)
REVERT: B  342 LEU cc_start: 0.8155 (mm) cc_final: 0.7757 (mm)
REVERT: C  412 MET cc_start: 0.6237 (ttt) cc_final: 0.5544 (tmm)
REVERT: C  416 ASN cc_start: 0.8720 (p0) cc_final: 0.8017 (p0)
REVERT: C  442 MET cc_start: 0.8669 (mmp) cc_final: 0.7957 (mtp)
REVERT: C  444 GLN cc_start: 0.8753 (mt0) cc_final: 0.8472 (mt0)
REVERT: C  473 ASN cc_start: 0.8788 (m110) cc_final: 0.8576 (m110)
REVERT: C  553 ASN cc_start: 0.8661 (t0) cc_final: 0.8336 (t0)
REVERT: D   94 MET cc_start: 0.7953 (mpp) cc_final: 0.7571 (mpp)
REVERT: D  209 PHE cc_start: 0.9115 (p90) cc_final: 0.8658 (p90)
REVERT: D  249 MET cc_start: 0.8389 (ppp) cc_final: 0.8162 (ppp)
REVERT: D  343 ILE cc_start: 0.8319 (mt) cc_final: 0.7950 (mt)
REVERT: D  378 THR cc_start: 0.7987 (m) cc_final: 0.7512 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.0642
  time to fit residues: 23.4480
Evaluate side-chains
  192 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 99 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0170
   chunk 2 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 67 optimal weight:    9.9990
   chunk 104 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 28 optimal weight:   20.0000
   chunk 62 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.1622

-------------------------------------------------------------------------------
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 = 0.3566 r_free = 0.3566 target = 0.098283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.077862 restraints weight = 26334.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.080305 restraints weight = 15047.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.082044 restraints weight = 10244.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.083208 restraints weight = 7829.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.083981 restraints weight = 6495.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8861  Z= 0.126
  Angle     :  0.648   8.712  11952  Z= 0.329
  Chirality :  0.047   0.192   1314
  Planarity :  0.004   0.033   1511
  Dihedral  :  4.939  31.117   1210
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.89 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.26), residues: 1055
  helix:  0.96 (0.24), residues: 477
  sheet: -0.03 (0.58), residues: 83
  loop : -0.37 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 563 
 TYR   0.016   0.001   TYR D 134 
 PHE   0.021   0.001   PHE A 390 
 TRP   0.020   0.001   TRP B 247 
 HIS   0.006   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8861)
  covalent geometry    : angle       0.64850 (11952)
  hydrogen bonds       : bond        0.03208 (  395)
  hydrogen bonds       : angle       5.00776 ( 1122)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 1416.52 seconds
wall clock time: 24 minutes 57.52 seconds (1497.52 seconds total)