Starting phenix.real_space_refine
on Wed Jan 15 21:22:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9axc_43932/01_2025/9axc_43932.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9axc_43932/01_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9axc_43932/01_2025/9axc_43932.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9axc_43932/01_2025/9axc_43932.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9axc_43932/01_2025/9axc_43932.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9axc_43932/01_2025/9axc_43932.cif"
  }
  resolution = 4.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.29, per 1000 atoms: 0.61
  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: 2.14
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.01
  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: 2.50

  Time building geometry restraints manager: 2.45 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 380 or resid 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:             0.530
  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:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.200
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.620
-------------------------------------------------------------------------------
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= 0.313
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (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
 TRP   0.040   0.002   TRP B 247 
 HIS   0.013   0.001   HIS A 477 
 PHE   0.040   0.003   PHE D 337 
 TYR   0.022   0.002   TYR B 229 
 ARG   0.056   0.002   ARG C 554 

*********************** 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  : 0.933 
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: 0.8156 (m-80)
REVERT: A  391 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8452 (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: 0.8628 (m-30)
REVERT: A  486 ASP cc_start: 0.8372 (t0) cc_final: 0.8115 (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: 0.7380 (mt-10)
REVERT: C  456 MET cc_start: 0.9305 (mmt) cc_final: 0.9081 (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: 0.8154 (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: 0.1989
  time to fit residues: 64.6840
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  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 80 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0670
   chunk 42 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   overall best weight:    1.3724

-------------------------------------------------------------------------------
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 = 0.3627 r_free = 0.3627 target = 0.103174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.082145 restraints weight = 25854.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.084617 restraints weight = 14990.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.086297 restraints weight = 10339.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1463

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= 0.191
  Angle     :  0.590   5.800  11952  Z= 0.311
  Chirality :  0.045   0.160   1314
  Planarity :  0.005   0.043   1511
  Dihedral  :  4.993  29.448   1210
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.13 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.25 %
    Favored  : 96.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.25), residues: 1055
  helix:  0.47 (0.24), residues: 469
  sheet:  0.46 (0.58), residues: 89
  loop : -0.69 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 247 
 HIS   0.010   0.001   HIS A 477 
 PHE   0.014   0.001   PHE D 337 
 TYR   0.013   0.001   TYR A 532 
 ARG   0.004   0.001   ARG D 363 

*********************** 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
  241 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 240
  time to evaluate  : 0.942 
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: 0.7712 (mmm) cc_final: 0.7316 (mmm)
REVERT: A  436 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7657 (tm-30)
REVERT: A  473 ASN cc_start: 0.8634 (m110) cc_final: 0.8260 (m110)
REVERT: A  486 ASP cc_start: 0.8571 (t0) cc_final: 0.8153 (t0)
REVERT: A  523 ASN cc_start: 0.8025 (t0) cc_final: 0.7574 (p0)
REVERT: A  532 TYR cc_start: 0.7904 (t80) cc_final: 0.7611 (t80)
REVERT: A  552 ASN cc_start: 0.7903 (p0) cc_final: 0.7607 (p0)
REVERT: B  182 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8275 (mm-30)
REVERT: B  253 LEU cc_start: 0.9232 (mm) cc_final: 0.8956 (mm)
REVERT: C  393 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7345 (mt-10)
REVERT: C  401 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7872 (mtp85)
REVERT: C  442 MET cc_start: 0.8623 (mmp) cc_final: 0.8389 (mtt)
REVERT: C  444 GLN cc_start: 0.8802 (mt0) cc_final: 0.8513 (mt0)
REVERT: C  469 MET cc_start: 0.8422 (mmp) cc_final: 0.8145 (tpp)
REVERT: C  481 THR cc_start: 0.8853 (m) cc_final: 0.8604 (m)
REVERT: D   94 MET cc_start: 0.8033 (mpp) cc_final: 0.7562 (mpp)
REVERT: D  199 ASN cc_start: 0.8834 (t0) cc_final: 0.8540 (t0)
REVERT: D  209 PHE cc_start: 0.8944 (p90) cc_final: 0.8661 (p90)
REVERT: D  240 TYR cc_start: 0.7320 (p90) cc_final: 0.6834 (p90)
REVERT: D  317 ILE cc_start: 0.9406 (mm) cc_final: 0.9196 (mm)
REVERT: D  343 ILE cc_start: 0.7813 (mt) cc_final: 0.7361 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1971
  time to fit residues: 65.9109
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  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0970
   chunk 8 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   chunk 90 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.3599 r_free = 0.3599 target = 0.101489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.080647 restraints weight = 26283.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.083150 restraints weight = 15143.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.084878 restraints weight = 10405.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8861  Z= 0.189
  Angle     :  0.561   5.899  11952  Z= 0.295
  Chirality :  0.045   0.146   1314
  Planarity :  0.004   0.047   1511
  Dihedral  :  4.755  29.998   1210
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.70 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.88 %
    Favored  : 96.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.26), residues: 1055
  helix:  0.89 (0.24), residues: 468
  sheet:  0.52 (0.61), residues: 79
  loop : -0.61 (0.27), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 247 
 HIS   0.008   0.001   HIS A 477 
 PHE   0.039   0.002   PHE A 387 
 TYR   0.012   0.001   TYR D 134 
 ARG   0.004   0.001   ARG D 363 

*********************** 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
  244 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 243
  time to evaluate  : 0.941 
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: 0.7612 (mmm) cc_final: 0.7099 (mmm)
REVERT: A  417 LEU cc_start: 0.8891 (mt) cc_final: 0.8424 (pt)
REVERT: A  436 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7704 (tm-30)
REVERT: A  486 ASP cc_start: 0.8423 (t0) cc_final: 0.7960 (t0)
REVERT: A  523 ASN cc_start: 0.8064 (t0) cc_final: 0.7822 (p0)
REVERT: A  552 ASN cc_start: 0.7961 (p0) cc_final: 0.7645 (p0)
REVERT: A  553 ASN cc_start: 0.9180 (t0) cc_final: 0.8840 (t0)
REVERT: B  182 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8285 (mm-30)
REVERT: B  190 ASP cc_start: 0.8245 (t0) cc_final: 0.7883 (t0)
REVERT: B  197 LEU cc_start: 0.8581 (mm) cc_final: 0.8347 (mm)
REVERT: B  253 LEU cc_start: 0.9258 (mm) cc_final: 0.8957 (mm)
REVERT: C  393 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7603 (mt-10)
REVERT: C  412 MET cc_start: 0.6853 (ttt) cc_final: 0.6641 (ttt)
REVERT: C  444 GLN cc_start: 0.8723 (mt0) cc_final: 0.8388 (mt0)
REVERT: C  456 MET cc_start: 0.9448 (mmm) cc_final: 0.9014 (mmt)
REVERT: C  458 TYR cc_start: 0.8976 (t80) cc_final: 0.8325 (t80)
REVERT: C  481 THR cc_start: 0.8987 (m) cc_final: 0.8750 (m)
REVERT: C  521 ASP cc_start: 0.7020 (t70) cc_final: 0.6627 (t70)
REVERT: C  553 ASN cc_start: 0.8625 (t0) cc_final: 0.8234 (t0)
REVERT: C  583 ARG cc_start: 0.8429 (tpm170) cc_final: 0.8115 (tpm170)
REVERT: D   94 MET cc_start: 0.8016 (mpp) cc_final: 0.7544 (mpp)
REVERT: D  199 ASN cc_start: 0.8963 (t0) cc_final: 0.8648 (t0)
REVERT: D  209 PHE cc_start: 0.9004 (p90) cc_final: 0.8712 (p90)
REVERT: D  308 MET cc_start: 0.4023 (ptp) cc_final: 0.3806 (mtm)
REVERT: D  317 ILE cc_start: 0.9393 (mm) cc_final: 0.9158 (mm)
REVERT: D  343 ILE cc_start: 0.7925 (mt) cc_final: 0.7299 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 243
  average time/residue: 0.1917
  time to fit residues: 64.8001
Evaluate side-chains
  178 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0170
   chunk 98 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 105 optimal weight:    0.0870
   chunk 90 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.9998

-------------------------------------------------------------------------------
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 = 0.3621 r_free = 0.3621 target = 0.102803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.082283 restraints weight = 25768.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.084811 restraints weight = 14803.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.086520 restraints weight = 10086.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2493

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= 0.160
  Angle     :  0.547   5.483  11952  Z= 0.286
  Chirality :  0.045   0.133   1314
  Planarity :  0.004   0.084   1511
  Dihedral  :  4.604  28.711   1210
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.41 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.26), residues: 1055
  helix:  1.11 (0.24), residues: 468
  sheet:  0.16 (0.64), residues: 71
  loop : -0.53 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 247 
 HIS   0.006   0.001   HIS A 477 
 PHE   0.023   0.001   PHE D 337 
 TYR   0.013   0.001   TYR D 134 
 ARG   0.008   0.000   ARG D 108 

*********************** 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
  240 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.978 
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: A  412 MET cc_start: 0.7738 (mmm) cc_final: 0.7066 (mmm)
REVERT: A  436 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7734 (tm-30)
REVERT: A  486 ASP cc_start: 0.8276 (t0) cc_final: 0.8037 (t70)
REVERT: A  552 ASN cc_start: 0.7961 (p0) cc_final: 0.7686 (p0)
REVERT: A  553 ASN cc_start: 0.9117 (t0) cc_final: 0.8702 (t0)
REVERT: B  182 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8351 (mm-30)
REVERT: B  190 ASP cc_start: 0.8328 (t0) cc_final: 0.7904 (t0)
REVERT: B  197 LEU cc_start: 0.8599 (mm) cc_final: 0.8375 (mm)
REVERT: B  253 LEU cc_start: 0.9215 (mm) cc_final: 0.8954 (mm)
REVERT: C  442 MET cc_start: 0.8801 (mmp) cc_final: 0.8192 (mtt)
REVERT: C  444 GLN cc_start: 0.8755 (mt0) cc_final: 0.8332 (mt0)
REVERT: C  521 ASP cc_start: 0.7075 (t70) cc_final: 0.6702 (t70)
REVERT: D   94 MET cc_start: 0.8233 (mpp) cc_final: 0.7858 (mpp)
REVERT: D  103 ILE cc_start: 0.9281 (mm) cc_final: 0.9058 (mm)
REVERT: D  134 TYR cc_start: 0.8391 (t80) cc_final: 0.8162 (t80)
REVERT: D  199 ASN cc_start: 0.9086 (t0) cc_final: 0.8647 (t0)
REVERT: D  209 PHE cc_start: 0.8734 (p90) cc_final: 0.8482 (p90)
REVERT: D  308 MET cc_start: 0.4598 (ptp) cc_final: 0.4332 (mtm)
REVERT: D  317 ILE cc_start: 0.9376 (mm) cc_final: 0.9122 (mm)
REVERT: D  343 ILE cc_start: 0.7988 (mt) cc_final: 0.7347 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1968
  time to fit residues: 67.1917
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  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0980
   chunk 47 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    3.4188

-------------------------------------------------------------------------------
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 = 0.3482 r_free = 0.3482 target = 0.094436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.074504 restraints weight = 27006.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.076907 restraints weight = 15432.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.078506 restraints weight = 10536.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   8861  Z= 0.382
  Angle     :  0.740  10.076  11952  Z= 0.382
  Chirality :  0.049   0.139   1314
  Planarity :  0.005   0.038   1511
  Dihedral  :  5.699  35.287   1210
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.17 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.25), residues: 1055
  helix:  0.59 (0.24), residues: 471
  sheet:  0.10 (0.69), residues: 54
  loop : -0.78 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP B 247 
 HIS   0.007   0.002   HIS C 466 
 PHE   0.024   0.002   PHE A 525 
 TYR   0.026   0.002   TYR C 534 
 ARG   0.016   0.001   ARG D 108 

*********************** 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
  213 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 1.040 
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: 0.8064 (mmm) cc_final: 0.6837 (mmm)
REVERT: A  436 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7861 (tm-30)
REVERT: A  447 ASP cc_start: 0.8997 (m-30) cc_final: 0.8780 (m-30)
REVERT: A  473 ASN cc_start: 0.9026 (m-40) cc_final: 0.8661 (m110)
REVERT: A  486 ASP cc_start: 0.8523 (t0) cc_final: 0.7596 (t0)
REVERT: A  504 GLN cc_start: 0.8287 (mm110) cc_final: 0.7248 (pm20)
REVERT: A  553 ASN cc_start: 0.9024 (t0) cc_final: 0.8645 (t0)
REVERT: B  182 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8554 (mm-30)
REVERT: B  188 HIS cc_start: 0.8168 (t70) cc_final: 0.7912 (t70)
REVERT: B  190 ASP cc_start: 0.8621 (t0) cc_final: 0.7765 (t0)
REVERT: B  197 LEU cc_start: 0.8896 (mm) cc_final: 0.8678 (mm)
REVERT: B  230 MET cc_start: 0.8289 (tpp) cc_final: 0.8056 (tpp)
REVERT: B  249 MET cc_start: 0.9047 (tmm) cc_final: 0.8804 (tmm)
REVERT: B  253 LEU cc_start: 0.9244 (mm) cc_final: 0.8901 (mm)
REVERT: B  314 LEU cc_start: 0.9205 (mt) cc_final: 0.8994 (mt)
REVERT: C  444 GLN cc_start: 0.8847 (mt0) cc_final: 0.8487 (mt0)
REVERT: C  458 TYR cc_start: 0.8911 (t80) cc_final: 0.8421 (t80)
REVERT: C  553 ASN cc_start: 0.8676 (t0) cc_final: 0.8328 (t0)
REVERT: D   94 MET cc_start: 0.7971 (mpp) cc_final: 0.7487 (mpp)
REVERT: D  209 PHE cc_start: 0.9151 (p90) cc_final: 0.8554 (p90)
REVERT: D  249 MET cc_start: 0.8917 (ppp) cc_final: 0.8594 (ppp)
REVERT: D  308 MET cc_start: 0.5295 (ptp) cc_final: 0.5018 (ptm)
REVERT: D  317 ILE cc_start: 0.9284 (mm) cc_final: 0.9042 (mt)
REVERT: D  327 SER cc_start: 0.8659 (p) cc_final: 0.8452 (p)
REVERT: D  378 THR cc_start: 0.8126 (m) cc_final: 0.7740 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1808
  time to fit residues: 54.9578
Evaluate side-chains
  167 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 103 optimal weight:    8.9990
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 = 0.3507 r_free = 0.3507 target = 0.096175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.075504 restraints weight = 26653.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.077963 restraints weight = 15306.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.079625 restraints weight = 10463.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8861  Z= 0.270
  Angle     :  0.631   8.025  11952  Z= 0.328
  Chirality :  0.046   0.133   1314
  Planarity :  0.004   0.036   1511
  Dihedral  :  5.286  33.033   1210
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.79 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.26), residues: 1055
  helix:  0.83 (0.24), residues: 471
  sheet: -0.28 (0.56), residues: 78
  loop : -0.75 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 247 
 HIS   0.018   0.002   HIS C 477 
 PHE   0.020   0.002   PHE D 337 
 TYR   0.023   0.002   TYR C 534 
 ARG   0.006   0.001   ARG D 234 

*********************** 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
  221 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.945 
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: 0.8155 (m-80) cc_final: 0.7492 (m-80)
REVERT: A  412 MET cc_start: 0.8493 (mmm) cc_final: 0.7681 (mmt)
REVERT: A  417 LEU cc_start: 0.9060 (mt) cc_final: 0.8785 (mt)
REVERT: A  436 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7842 (tm-30)
REVERT: A  447 ASP cc_start: 0.9063 (m-30) cc_final: 0.8820 (m-30)
REVERT: A  473 ASN cc_start: 0.8940 (m-40) cc_final: 0.8563 (m-40)
REVERT: A  486 ASP cc_start: 0.8289 (t0) cc_final: 0.7423 (t0)
REVERT: A  504 GLN cc_start: 0.8141 (mm110) cc_final: 0.7029 (pm20)
REVERT: A  508 SER cc_start: 0.8388 (m) cc_final: 0.8181 (t)
REVERT: A  532 TYR cc_start: 0.8825 (t80) cc_final: 0.8624 (t80)
REVERT: A  552 ASN cc_start: 0.7350 (p0) cc_final: 0.7129 (p0)
REVERT: A  553 ASN cc_start: 0.9058 (t0) cc_final: 0.8647 (t0)
REVERT: B  187 MET cc_start: 0.8111 (pmm) cc_final: 0.7880 (pmm)
REVERT: B  190 ASP cc_start: 0.8668 (t0) cc_final: 0.7679 (t0)
REVERT: B  197 LEU cc_start: 0.8880 (mm) cc_final: 0.8642 (mm)
REVERT: B  249 MET cc_start: 0.9134 (tmm) cc_final: 0.8802 (tmm)
REVERT: B  253 LEU cc_start: 0.9250 (mm) cc_final: 0.8970 (mm)
REVERT: C  442 MET cc_start: 0.8833 (mmp) cc_final: 0.7989 (mtp)
REVERT: C  444 GLN cc_start: 0.8882 (mt0) cc_final: 0.8481 (mt0)
REVERT: C  458 TYR cc_start: 0.8917 (t80) cc_final: 0.8377 (t80)
REVERT: C  521 ASP cc_start: 0.7281 (t70) cc_final: 0.6940 (t70)
REVERT: D   94 MET cc_start: 0.8283 (mpp) cc_final: 0.7978 (mpp)
REVERT: D  209 PHE cc_start: 0.9169 (p90) cc_final: 0.8615 (p90)
REVERT: D  249 MET cc_start: 0.8620 (ppp) cc_final: 0.8285 (ppp)
REVERT: D  317 ILE cc_start: 0.9273 (mm) cc_final: 0.9038 (mt)
REVERT: D  343 ILE cc_start: 0.8400 (mt) cc_final: 0.8057 (mt)
REVERT: D  378 THR cc_start: 0.7907 (m) cc_final: 0.7537 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.1780
  time to fit residues: 56.3869
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  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 90 optimal weight:    0.3980
   chunk 5 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 104 optimal weight:    0.0980
   chunk 91 optimal weight:    0.4980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3534 r_free = 0.3534 target = 0.097873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.077254 restraints weight = 26316.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.079694 restraints weight = 15140.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.081329 restraints weight = 10372.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3852

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= 0.181
  Angle     :  0.597   9.202  11952  Z= 0.306
  Chirality :  0.045   0.127   1314
  Planarity :  0.004   0.042   1511
  Dihedral  :  4.924  31.694   1210
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.79 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.26), residues: 1055
  helix:  1.00 (0.24), residues: 472
  sheet: -0.02 (0.60), residues: 69
  loop : -0.60 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 247 
 HIS   0.014   0.001   HIS C 477 
 PHE   0.023   0.001   PHE A 390 
 TYR   0.026   0.002   TYR C 534 
 ARG   0.007   0.001   ARG A 563 

*********************** 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
  229 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 MET cc_start: 0.8495 (mmm) cc_final: 0.7747 (mmt)
REVERT: A  436 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7728 (tm-30)
REVERT: A  441 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8458 (tm-30)
REVERT: A  473 ASN cc_start: 0.8922 (m-40) cc_final: 0.8181 (m-40)
REVERT: A  486 ASP cc_start: 0.8304 (t0) cc_final: 0.7295 (t0)
REVERT: A  504 GLN cc_start: 0.8134 (mm110) cc_final: 0.7022 (pm20)
REVERT: A  532 TYR cc_start: 0.8698 (t80) cc_final: 0.8395 (t80)
REVERT: A  553 ASN cc_start: 0.9069 (t0) cc_final: 0.8802 (t0)
REVERT: B  182 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8661 (mm-30)
REVERT: B  190 ASP cc_start: 0.8601 (t0) cc_final: 0.7691 (t0)
REVERT: B  192 LYS cc_start: 0.9246 (pttt) cc_final: 0.8919 (ptmm)
REVERT: B  229 TYR cc_start: 0.8888 (m-80) cc_final: 0.8671 (m-80)
REVERT: B  249 MET cc_start: 0.9158 (tmm) cc_final: 0.8852 (tmm)
REVERT: B  253 LEU cc_start: 0.9151 (mm) cc_final: 0.8785 (mm)
REVERT: C  412 MET cc_start: 0.7009 (tmm) cc_final: 0.6608 (tmm)
REVERT: C  416 ASN cc_start: 0.8639 (p0) cc_final: 0.8392 (p0)
REVERT: C  442 MET cc_start: 0.8737 (mmp) cc_final: 0.7981 (mtp)
REVERT: C  444 GLN cc_start: 0.8771 (mt0) cc_final: 0.8411 (mt0)
REVERT: C  458 TYR cc_start: 0.8920 (t80) cc_final: 0.8408 (t80)
REVERT: C  469 MET cc_start: 0.9182 (tpp) cc_final: 0.8958 (tpp)
REVERT: C  521 ASP cc_start: 0.7287 (t70) cc_final: 0.6919 (t70)
REVERT: C  553 ASN cc_start: 0.8649 (t0) cc_final: 0.8336 (t0)
REVERT: D  209 PHE cc_start: 0.9136 (p90) cc_final: 0.8635 (p90)
REVERT: D  249 MET cc_start: 0.8686 (ppp) cc_final: 0.8405 (ppp)
REVERT: D  317 ILE cc_start: 0.9377 (mm) cc_final: 0.9117 (mt)
REVERT: D  343 ILE cc_start: 0.8255 (mt) cc_final: 0.7865 (mt)
REVERT: D  378 THR cc_start: 0.7877 (m) cc_final: 0.7510 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1708
  time to fit residues: 56.9445
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  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 103 optimal weight:    5.9990
   chunk 3 optimal weight:    0.3980
   chunk 28 optimal weight:   10.0000
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.098336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.077289 restraints weight = 26516.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.079806 restraints weight = 14881.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.081500 restraints weight = 10102.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3995

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= 0.184
  Angle     :  0.609   8.042  11952  Z= 0.310
  Chirality :  0.046   0.182   1314
  Planarity :  0.004   0.034   1511
  Dihedral  :  4.835  31.263   1210
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.89 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.26), residues: 1055
  helix:  1.04 (0.24), residues: 472
  sheet: -0.01 (0.57), residues: 73
  loop : -0.48 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 247 
 HIS   0.012   0.001   HIS C 477 
 PHE   0.024   0.001   PHE D 337 
 TYR   0.024   0.001   TYR C 534 
 ARG   0.009   0.001   ARG A 563 

*********************** 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
  235 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 PHE cc_start: 0.8171 (m-80) cc_final: 0.7721 (m-80)
REVERT: A  390 PHE cc_start: 0.8107 (t80) cc_final: 0.7856 (t80)
REVERT: A  412 MET cc_start: 0.8575 (mmm) cc_final: 0.7741 (mmt)
REVERT: A  417 LEU cc_start: 0.8904 (mt) cc_final: 0.8688 (mt)
REVERT: A  436 GLN cc_start: 0.8340 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: A  441 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8516 (tm-30)
REVERT: A  473 ASN cc_start: 0.8885 (m-40) cc_final: 0.8071 (m110)
REVERT: A  486 ASP cc_start: 0.8294 (t0) cc_final: 0.7232 (t0)
REVERT: A  504 GLN cc_start: 0.8144 (mm110) cc_final: 0.6983 (pm20)
REVERT: A  532 TYR cc_start: 0.8727 (t80) cc_final: 0.8402 (t80)
REVERT: A  553 ASN cc_start: 0.9137 (t0) cc_final: 0.8901 (t0)
REVERT: B  182 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8654 (mm-30)
REVERT: B  190 ASP cc_start: 0.8509 (t0) cc_final: 0.7675 (t0)
REVERT: B  249 MET cc_start: 0.9224 (tmm) cc_final: 0.8898 (tmm)
REVERT: B  253 LEU cc_start: 0.9196 (mm) cc_final: 0.8678 (mm)
REVERT: B  324 LYS cc_start: 0.4730 (mmtt) cc_final: 0.4057 (mmtt)
REVERT: C  412 MET cc_start: 0.7295 (tmm) cc_final: 0.6917 (tmm)
REVERT: C  416 ASN cc_start: 0.8639 (p0) cc_final: 0.8361 (p0)
REVERT: C  444 GLN cc_start: 0.8780 (mt0) cc_final: 0.8447 (mt0)
REVERT: C  458 TYR cc_start: 0.8904 (t80) cc_final: 0.8442 (t80)
REVERT: C  493 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8407 (mtpp)
REVERT: C  521 ASP cc_start: 0.7714 (t70) cc_final: 0.7340 (t70)
REVERT: C  553 ASN cc_start: 0.8633 (t0) cc_final: 0.8343 (t0)
REVERT: C  577 CYS cc_start: 0.7960 (m) cc_final: 0.7459 (t)
REVERT: D   94 MET cc_start: 0.8031 (mpp) cc_final: 0.7611 (mpp)
REVERT: D  209 PHE cc_start: 0.9138 (p90) cc_final: 0.8650 (p90)
REVERT: D  249 MET cc_start: 0.8670 (ppp) cc_final: 0.8400 (ppp)
REVERT: D  317 ILE cc_start: 0.9369 (mm) cc_final: 0.9128 (mt)
REVERT: D  343 ILE cc_start: 0.8255 (mt) cc_final: 0.7839 (mt)
REVERT: D  378 THR cc_start: 0.7918 (m) cc_final: 0.7530 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.1700
  time to fit residues: 58.1743
Evaluate side-chains
  185 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 102 optimal weight:    0.4980
   chunk 82 optimal weight:    1.9990
   chunk 93 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.099075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.078461 restraints weight = 25998.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.080950 restraints weight = 14720.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.082640 restraints weight = 10016.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.4009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8861  Z= 0.167
  Angle     :  0.634  10.108  11952  Z= 0.322
  Chirality :  0.046   0.161   1314
  Planarity :  0.004   0.034   1511
  Dihedral  :  4.781  30.282   1210
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.70 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.26), residues: 1055
  helix:  1.12 (0.25), residues: 472
  sheet:  0.08 (0.62), residues: 63
  loop : -0.37 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 247 
 HIS   0.011   0.001   HIS C 477 
 PHE   0.015   0.001   PHE A 443 
 TYR   0.009   0.001   TYR D 134 
 ARG   0.008   0.001   ARG A 563 

*********************** 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
  233 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.927 
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  387 PHE cc_start: 0.8159 (m-80) cc_final: 0.7687 (m-80)
REVERT: A  412 MET cc_start: 0.8593 (mmm) cc_final: 0.7819 (mmt)
REVERT: A  417 LEU cc_start: 0.8923 (mt) cc_final: 0.8408 (pt)
REVERT: A  436 GLN cc_start: 0.8378 (tm-30) cc_final: 0.7891 (tm-30)
REVERT: A  442 MET cc_start: 0.8717 (mpp) cc_final: 0.8227 (mmt)
REVERT: A  473 ASN cc_start: 0.8811 (m-40) cc_final: 0.8112 (m110)
REVERT: A  486 ASP cc_start: 0.8226 (t0) cc_final: 0.7157 (t0)
REVERT: A  504 GLN cc_start: 0.8033 (mm110) cc_final: 0.6798 (pm20)
REVERT: A  532 TYR cc_start: 0.8687 (t80) cc_final: 0.8432 (t80)
REVERT: A  552 ASN cc_start: 0.7239 (p0) cc_final: 0.7032 (p0)
REVERT: A  553 ASN cc_start: 0.9175 (t0) cc_final: 0.8937 (t0)
REVERT: B  111 ILE cc_start: 0.9144 (mt) cc_final: 0.8809 (mt)
REVERT: B  182 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8803 (mm-30)
REVERT: B  190 ASP cc_start: 0.8325 (t0) cc_final: 0.7710 (t0)
REVERT: B  197 LEU cc_start: 0.8554 (mm) cc_final: 0.8332 (mm)
REVERT: B  249 MET cc_start: 0.9258 (tmm) cc_final: 0.8995 (tmm)
REVERT: B  253 LEU cc_start: 0.9193 (mm) cc_final: 0.8827 (mm)
REVERT: B  324 LYS cc_start: 0.4929 (mmtt) cc_final: 0.4580 (mmtt)
REVERT: C  367 LYS cc_start: 0.9256 (mmmm) cc_final: 0.8964 (mppt)
REVERT: C  412 MET cc_start: 0.6988 (tmm) cc_final: 0.6529 (tmm)
REVERT: C  414 LYS cc_start: 0.8852 (tptp) cc_final: 0.8550 (pttt)
REVERT: C  442 MET cc_start: 0.8726 (mmp) cc_final: 0.7973 (mtp)
REVERT: C  444 GLN cc_start: 0.8810 (mt0) cc_final: 0.8462 (mt0)
REVERT: C  457 ASP cc_start: 0.8923 (t70) cc_final: 0.8658 (t70)
REVERT: C  458 TYR cc_start: 0.8894 (t80) cc_final: 0.8327 (t80)
REVERT: C  473 ASN cc_start: 0.8660 (m110) cc_final: 0.8382 (m110)
REVERT: C  493 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8493 (mtpt)
REVERT: C  521 ASP cc_start: 0.7747 (t70) cc_final: 0.7543 (t70)
REVERT: C  577 CYS cc_start: 0.7996 (m) cc_final: 0.7458 (t)
REVERT: D   94 MET cc_start: 0.8036 (mpp) cc_final: 0.7590 (mpp)
REVERT: D  209 PHE cc_start: 0.9107 (p90) cc_final: 0.8655 (p90)
REVERT: D  249 MET cc_start: 0.8498 (ppp) cc_final: 0.8122 (ppp)
REVERT: D  317 ILE cc_start: 0.9368 (mm) cc_final: 0.9132 (mt)
REVERT: D  343 ILE cc_start: 0.8203 (mt) cc_final: 0.7698 (mt)
REVERT: D  378 THR cc_start: 0.7950 (m) cc_final: 0.7514 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.1829
  time to fit residues: 61.5307
Evaluate side-chains
  190 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0170
   chunk 66 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 93 optimal weight:    0.2980
   chunk 42 optimal weight:    8.9990
   chunk 34 optimal weight:    9.9990
   chunk 104 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.2422

-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.098148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.077246 restraints weight = 26215.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.079715 restraints weight = 14720.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.081491 restraints weight = 9995.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.4131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8861  Z= 0.188
  Angle     :  0.648   9.469  11952  Z= 0.329
  Chirality :  0.046   0.175   1314
  Planarity :  0.004   0.033   1511
  Dihedral  :  4.867  30.458   1210
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.89 %
    Favored  : 95.92 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.26), residues: 1055
  helix:  1.12 (0.24), residues: 472
  sheet:  0.12 (0.58), residues: 73
  loop : -0.44 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 247 
 HIS   0.011   0.001   HIS C 477 
 PHE   0.022   0.002   PHE D 337 
 TYR   0.027   0.001   TYR C 534 
 ARG   0.008   0.001   ARG A 563 

********************** 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
  227 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  412 MET cc_start: 0.8632 (mmm) cc_final: 0.7956 (mmp)
REVERT: A  436 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7902 (tm-30)
REVERT: A  441 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8571 (tm-30)
REVERT: A  486 ASP cc_start: 0.8239 (t0) cc_final: 0.7254 (t0)
REVERT: A  504 GLN cc_start: 0.8077 (mm110) cc_final: 0.6767 (pp30)
REVERT: A  532 TYR cc_start: 0.8682 (t80) cc_final: 0.8381 (t80)
REVERT: A  552 ASN cc_start: 0.7306 (p0) cc_final: 0.7094 (p0)
REVERT: A  553 ASN cc_start: 0.9140 (t0) cc_final: 0.8910 (t0)
REVERT: B  111 ILE cc_start: 0.9181 (mt) cc_final: 0.8811 (mt)
REVERT: B  182 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8783 (mm-30)
REVERT: B  183 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8634 (ttmt)
REVERT: B  190 ASP cc_start: 0.8362 (t0) cc_final: 0.7773 (t0)
REVERT: B  197 LEU cc_start: 0.8581 (mm) cc_final: 0.8356 (mm)
REVERT: B  249 MET cc_start: 0.9304 (tmm) cc_final: 0.8949 (tmm)
REVERT: B  253 LEU cc_start: 0.9242 (mm) cc_final: 0.8859 (mm)
REVERT: B  324 LYS cc_start: 0.5035 (mmtt) cc_final: 0.4696 (mmtt)
REVERT: B  342 LEU cc_start: 0.8034 (mm) cc_final: 0.7581 (mm)
REVERT: C  412 MET cc_start: 0.7122 (tmm) cc_final: 0.6687 (tmm)
REVERT: C  442 MET cc_start: 0.8773 (mmp) cc_final: 0.7998 (mtp)
REVERT: C  444 GLN cc_start: 0.8885 (mt0) cc_final: 0.8506 (mt0)
REVERT: C  458 TYR cc_start: 0.8926 (t80) cc_final: 0.8313 (t80)
REVERT: C  521 ASP cc_start: 0.7716 (t70) cc_final: 0.7490 (t70)
REVERT: C  538 LEU cc_start: 0.9353 (mt) cc_final: 0.9000 (mt)
REVERT: C  577 CYS cc_start: 0.8063 (m) cc_final: 0.7535 (t)
REVERT: D   94 MET cc_start: 0.8111 (mpp) cc_final: 0.7723 (mpp)
REVERT: D  209 PHE cc_start: 0.9097 (p90) cc_final: 0.8690 (p90)
REVERT: D  317 ILE cc_start: 0.9458 (mm) cc_final: 0.9233 (mt)
REVERT: D  343 ILE cc_start: 0.8223 (mt) cc_final: 0.7704 (mt)
REVERT: D  378 THR cc_start: 0.7978 (m) cc_final: 0.7564 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.1712
  time to fit residues: 56.3375
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  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 100 optimal weight:    0.3980
   chunk 48 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0270
   chunk 29 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 76 optimal weight:    6.9990
   overall best weight:    0.5238

-------------------------------------------------------------------------------
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 = 0.3588 r_free = 0.3588 target = 0.100053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.079461 restraints weight = 26255.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.082065 restraints weight = 14854.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.083821 restraints weight = 10042.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.4154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8861  Z= 0.156
  Angle     :  0.639  10.303  11952  Z= 0.323
  Chirality :  0.046   0.165   1314
  Planarity :  0.004   0.033   1511
  Dihedral  :  4.733  29.363   1210
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.51 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.26), residues: 1055
  helix:  1.13 (0.25), residues: 472
  sheet: -0.13 (0.58), residues: 79
  loop : -0.45 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 247 
 HIS   0.008   0.001   HIS C 477 
 PHE   0.020   0.001   PHE A 390 
 TYR   0.011   0.001   TYR D 125 
 ARG   0.007   0.001   ARG A 563 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 2502.63 seconds
wall clock time: 45 minutes 34.48 seconds (2734.48 seconds total)