Starting phenix.real_space_refine
on Tue Mar  3 12:09:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8afl_15401/03_2026/8afl_15401.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8afl_15401/03_2026/8afl_15401.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8afl_15401/03_2026/8afl_15401.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8afl_15401/03_2026/8afl_15401.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8afl_15401/03_2026/8afl_15401.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8afl_15401/03_2026/8afl_15401.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2377      2.51       5
     N     746      2.21       5
     O     784      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3921
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 605
          Classifications: {'peptide': 77}
          Link IDs: {'TRANS': 76}
    Chain: "B"
      Number of atoms: 605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 605
          Classifications: {'peptide': 77}
          Link IDs: {'TRANS': 76}
    Chain: "D"
      Number of atoms: 869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 869
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 2, 'TRANS': 109}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 869
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 2, 'TRANS': 109}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 518
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
    Chain: "F"
      Number of atoms: 455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 455
          Classifications: {'peptide': 59}
          Link IDs: {'TRANS': 58}
  Time building chain proxies: 0.83, per 1000 atoms: 0.21
  Number of scatterers: 3921
  At special positions: 0
  Unit cell: (164.16, 81.216, 86.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     784      8.00
     N     746      7.00
     C    2377      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 795 " - pdb=" SG  CYS D 868 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 795 " - pdb=" SG  CYS C 868 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.32
  Conformation dependent library (CDL) restraints added in 164.1 milliseconds
  

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  954

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 6 sheets defined
      58.2% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 369 through 419
      removed outlier: 3.537A  pdb=" N   LYS A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU A 378 " --> pdb=" O   GLN A 374 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   GLU A 382 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA A 390 " --> pdb=" O   GLN A 386 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ARG A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLN A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   GLU A 397 " --> pdb=" O   ASP A 393 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   VAL A 402 " --> pdb=" O   ALA A 398 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLU A 407 " --> pdb=" O   ARG A 403 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA A 408 " --> pdb=" O   ARG A 404 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   ILE A 410 " --> pdb=" O   HIS A 406 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ALA A 411 " --> pdb=" O   GLU A 407 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   THR A 416 " --> pdb=" O   GLU A 412 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE A 417 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 434
      removed outlier: 3.766A  pdb=" N   LEU A 426 " --> pdb=" O   SER A 422 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   GLU A 428 " --> pdb=" O   ALA A 424 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ALA A 430 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LEU A 431 " --> pdb=" O   ALA A 427 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A 434 " --> pdb=" O   ALA A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 443
      removed outlier: 4.228A  pdb=" N   LEU A 441 " --> pdb=" O   ASP A 437 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   MET A 443 " --> pdb=" O   SER A 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 401
      removed outlier: 3.846A  pdb=" N   LYS B 379 " --> pdb=" O   GLU B 375 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ARG B 380 " --> pdb=" O   LYS B 376 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ALA B 381 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU B 383 " --> pdb=" O   LYS B 379 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN B 386 " --> pdb=" O   GLU B 382 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ARG B 391 " --> pdb=" O   GLN B 387 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU B 392 " --> pdb=" O   LEU B 388 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLN B 399 " --> pdb=" O   MET B 395 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASP B 400 " --> pdb=" O   GLN B 396 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLN B 401 " --> pdb=" O   GLU B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 429
      removed outlier: 3.516A  pdb=" N   ALA B 408 " --> pdb=" O   ARG B 404 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ILE B 410 " --> pdb=" O   HIS B 406 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA B 411 " --> pdb=" O   GLU B 407 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   THR B 416 " --> pdb=" O   GLU B 412 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ILE B 417 " --> pdb=" O   LEU B 413 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLU B 418 " --> pdb=" O   GLN B 414 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   THR B 421 " --> pdb=" O   ILE B 417 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU B 426 " --> pdb=" O   SER B 422 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLY B 429 " --> pdb=" O   ALA B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 434
      removed outlier: 3.606A  pdb=" N   ALA B 434 " --> pdb=" O   ALA B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 439
    Processing helix  chain 'B' and resid 440 through 443
    Processing helix  chain 'D' and resid 833 through 837
      removed outlier: 3.505A  pdb=" N   LYS D 837 " --> pdb=" O   ASP D 834 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 859 through 863
      removed outlier: 4.110A  pdb=" N   THR D 863 " --> pdb=" O   PRO D 860 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 859 through 863
      removed outlier: 3.537A  pdb=" N   THR C 863 " --> pdb=" O   PRO C 860 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 97 through 155
      removed outlier: 3.911A  pdb=" N   GLN E 105 " --> pdb=" O   ILE E 101 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA E 106 " --> pdb=" O   ALA E 102 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER E 112 " --> pdb=" O   GLU E 108 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   ALA E 116 " --> pdb=" O   SER E 112 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLU E 124 " --> pdb=" O   THR E 120 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU E 137 " --> pdb=" O   ASP E 133 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ARG E 145 " --> pdb=" O   LEU E 141 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU E 146 " --> pdb=" O   GLU E 142 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU E 155 " --> pdb=" O   LEU E 151 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 155 through 160
      removed outlier: 3.631A  pdb=" N   SER E 159 " --> pdb=" O   LEU E 155 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 161 through 163
      No H-bonds generated for 'chain 'E' and resid 161 through 163'
    Processing helix  chain 'F' and resid 97 through 139
      removed outlier: 3.523A  pdb=" N   LEU F 103 " --> pdb=" O   ARG F  99 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA F 106 " --> pdb=" O   ALA F 102 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   GLU F 124 " --> pdb=" O   THR F 120 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   SER F 125 " --> pdb=" O   ALA F 121 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ASN F 139 " --> pdb=" O   ALA F 135 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 139 through 154
      removed outlier: 3.893A  pdb=" N   ILE F 143 " --> pdb=" O   ASN F 139 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP F 144 " --> pdb=" O   ALA F 140 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ASN F 148 " --> pdb=" O   ASP F 144 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   SER F 153 " --> pdb=" O   ALA F 149 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7
      removed outlier: 4.036A  pdb=" N   CYS D 795 " --> pdb=" O   VAL D 851 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL D 851 " --> pdb=" O   CYS D 795 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ILE D 841 " --> pdb=" O   GLN D 854 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 818 through 824
      removed outlier: 3.562A  pdb=" N   GLY D 819 " --> pdb=" O   ARG D 811 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   TRP D 809 " --> pdb=" O   VAL D 821 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   VAL D 823 " --> pdb=" O   MET D 807 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   MET D 807 " --> pdb=" O   VAL D 823 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 869 through 872
      removed outlier: 3.693A  pdb=" N   ALA D 870 " --> pdb=" O   TYR D 877 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 790 through 795
      removed outlier: 3.516A  pdb=" N   CYS C 795 " --> pdb=" O   VAL C 851 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 830 through 832
      removed outlier: 3.632A  pdb=" N   ASN C 831 " --> pdb=" O   VAL C 823 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL C 823 " --> pdb=" O   ASN C 831 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL C 821 " --> pdb=" O   TRP C 809 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   TRP C 809 " --> pdb=" O   VAL C 821 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   VAL C 823 " --> pdb=" O   MET C 807 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   MET C 807 " --> pdb=" O   VAL C 823 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA C 870 " --> pdb=" O   TYR C 877 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 830 through 832
      removed outlier: 3.632A  pdb=" N   ASN C 831 " --> pdb=" O   VAL C 823 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL C 823 " --> pdb=" O   ASN C 831 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL C 821 " --> pdb=" O   TRP C 809 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   TRP C 809 " --> pdb=" O   VAL C 821 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   VAL C 823 " --> pdb=" O   MET C 807 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   MET C 807 " --> pdb=" O   VAL C 823 " (cutoff:3.500A)

    217 hydrogen bonds defined for protein.
    618 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: 0.41

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1423
        1.34 -     1.46: 597
        1.46 -     1.58: 1903
        1.58 -     1.70: 0
        1.70 -     1.81: 24
  Bond restraints: 3947
  Sorted by residual:
  bond pdb=" N   ARG E 114 "
       pdb=" CA  ARG E 114 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.73e+00
  bond pdb=" N   LEU E 115 "
       pdb=" CA  LEU E 115 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.20e-02 6.94e+03 5.62e+00
  bond pdb=" N   ALA E 113 "
       pdb=" CA  ALA E 113 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.025 1.29e-02 6.01e+03 3.64e+00
  bond pdb=" N   ALA E 116 "
       pdb=" CA  ALA E 116 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.023 1.23e-02 6.61e+03 3.54e+00
  bond pdb=" CA  ALA E 116 "
       pdb=" CB  ALA E 116 "
    ideal  model  delta    sigma   weight residual
    1.528  1.508  0.020 1.59e-02 3.96e+03 1.61e+00
  ... (remaining 3942 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 5092
        1.72 -     3.44: 187
        3.44 -     5.15: 18
        5.15 -     6.87: 4
        6.87 -     8.59: 2
  Bond angle restraints: 5303
  Sorted by residual:
  angle pdb=" N   GLY C 803 "
        pdb=" CA  GLY C 803 "
        pdb=" C   GLY C 803 "
      ideal   model   delta    sigma   weight residual
     113.18  106.25    6.93 2.37e+00 1.78e-01 8.55e+00
  angle pdb=" N   ALA C 864 "
        pdb=" CA  ALA C 864 "
        pdb=" C   ALA C 864 "
      ideal   model   delta    sigma   weight residual
     107.88  111.56   -3.68 1.41e+00 5.03e-01 6.80e+00
  angle pdb=" CA  ARG E  99 "
        pdb=" CB  ARG E  99 "
        pdb=" CG  ARG E  99 "
      ideal   model   delta    sigma   weight residual
     114.10  119.30   -5.20 2.00e+00 2.50e-01 6.75e+00
  angle pdb=" CA  ALA E 116 "
        pdb=" C   ALA E 116 "
        pdb=" O   ALA E 116 "
      ideal   model   delta    sigma   weight residual
     120.42  117.74    2.68 1.06e+00 8.90e-01 6.40e+00
  angle pdb=" N   SER E 112 "
        pdb=" CA  SER E 112 "
        pdb=" C   SER E 112 "
      ideal   model   delta    sigma   weight residual
     112.54  109.47    3.07 1.22e+00 6.72e-01 6.32e+00
  ... (remaining 5298 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 2207
       17.76 -    35.51: 205
       35.51 -    53.27: 44
       53.27 -    71.02: 6
       71.02 -    88.78: 9
  Dihedral angle restraints: 2471
    sinusoidal: 1006
      harmonic: 1465
  Sorted by residual:
  dihedral pdb=" CB  CYS C 795 "
           pdb=" SG  CYS C 795 "
           pdb=" SG  CYS C 868 "
           pdb=" CB  CYS C 868 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.67   45.33     1      1.00e+01 1.00e-02 2.85e+01
  dihedral pdb=" CA  ILE D 804 "
           pdb=" C   ILE D 804 "
           pdb=" N   ASN D 805 "
           pdb=" CA  ASN D 805 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.25   23.75     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  ASP C 802 "
           pdb=" C   ASP C 802 "
           pdb=" N   GLY C 803 "
           pdb=" CA  GLY C 803 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.83   22.17     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 2468 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 341
       0.028 -    0.056: 152
       0.056 -    0.084: 64
       0.084 -    0.112: 23
       0.112 -    0.140: 16
  Chirality restraints: 596
  Sorted by residual:
  chirality pdb=" CA  ASN D 857 "
            pdb=" N   ASN D 857 "
            pdb=" C   ASN D 857 "
            pdb=" CB  ASN D 857 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.87e-01
  chirality pdb=" CA  LEU E 115 "
            pdb=" N   LEU E 115 "
            pdb=" C   LEU E 115 "
            pdb=" CB  LEU E 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.86e-01
  chirality pdb=" CA  ILE D 841 "
            pdb=" N   ILE D 841 "
            pdb=" C   ILE D 841 "
            pdb=" CB  ILE D 841 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  ... (remaining 593 not shown)

  Planarity restraints: 708
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 827 "    0.015 2.00e-02 2.50e+03   9.50e-03 2.26e+00
        pdb=" CG  TRP D 827 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 827 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 827 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 827 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 827 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 827 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 827 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 827 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 827 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 809 "   -0.013 2.00e-02 2.50e+03   8.86e-03 1.96e+00
        pdb=" CG  TRP C 809 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 809 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 809 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 809 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 809 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 809 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 809 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 809 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 809 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 380 "   -0.034 9.50e-02 1.11e+02   1.84e-02 1.45e+00
        pdb=" NE  ARG B 380 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 380 "   -0.019 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 380 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 380 "    0.005 2.00e-02 2.50e+03
  ... (remaining 705 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 157
        2.70 -     3.25: 4226
        3.25 -     3.80: 5850
        3.80 -     4.35: 7592
        4.35 -     4.90: 11630
  Nonbonded interactions: 29455
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN D 883 "
            pdb=" OG1 THR D 885 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" O   LEU C 791 "
            pdb=" NE2 GLN C 854 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" O   LEU E 160 "
            pdb=" OG  SER E 163 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" NH2 ARG A 419 "
            pdb=" O   GLY C 874 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" N   ASP C 802 "
            pdb=" OD2 ASP C 849 "
     model   vdw
     2.248 3.120
  ... (remaining 29450 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'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = (chain 'E' and resid 96 through 154)
  selection = chain 'F'
}

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:             1.220
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.070
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5871
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3949  Z= 0.213
  Angle     :  0.743   8.590   5307  Z= 0.446
  Chirality :  0.042   0.140    596
  Planarity :  0.003   0.029    708
  Dihedral  : 15.272  88.780   1511
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 18.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.25 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.48 (0.35), residues: 489
  helix: -2.28 (0.28), residues: 252
  sheet: -2.15 (0.56), residues: 83
  loop : -1.97 (0.49), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG B 380 
 TYR   0.019   0.002   TYR C 872 
 PHE   0.010   0.003   PHE D 840 
 TRP   0.025   0.004   TRP D 827 
 HIS   0.002   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 3947)
  covalent geometry    : angle       0.74208 ( 5303)
  SS BOND              : bond        0.00646 (    2)
  SS BOND              : angle       1.34307 (    4)
  hydrogen bonds       : bond        0.30317 (  209)
  hydrogen bonds       : angle      11.34174 (  618)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  392 LEU cc_start: 0.8152 (tp) cc_final: 0.7539 (tt)
REVERT: D  802 ASP cc_start: 0.6957 (t0) cc_final: 0.6697 (t0)
REVERT: D  857 ASN cc_start: 0.3871 (p0) cc_final: 0.3542 (p0)
REVERT: C  793 LEU cc_start: 0.6164 (mt) cc_final: 0.5809 (mt)
REVERT: E  156 LYS cc_start: 0.6778 (mtmt) cc_final: 0.6500 (mtmt)
REVERT: F  124 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7757 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 104
  average time/residue: 0.1113
  time to fit residues: 13.3608
Evaluate side-chains
  96 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0870
   chunk 30 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
D 854 GLN
C 805 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.182999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.171879 restraints weight = 9259.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.173533 restraints weight = 6660.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.174690 restraints weight = 5030.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.175377 restraints weight = 3985.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.176076 restraints weight = 3362.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.4315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5720
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3949  Z= 0.145
  Angle     :  0.645   7.867   5307  Z= 0.337
  Chirality :  0.042   0.153    596
  Planarity :  0.004   0.034    708
  Dihedral  :  5.304  21.774    563
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.37), residues: 489
  helix: -0.90 (0.31), residues: 249
  sheet: -2.14 (0.64), residues: 65
  loop : -1.43 (0.48), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 129 
 TYR   0.012   0.001   TYR C 872 
 PHE   0.005   0.001   PHE D 840 
 TRP   0.019   0.002   TRP C 809 
 HIS   0.003   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3947)
  covalent geometry    : angle       0.64461 ( 5303)
  SS BOND              : bond        0.00460 (    2)
  SS BOND              : angle       1.01173 (    4)
  hydrogen bonds       : bond        0.04900 (  209)
  hydrogen bonds       : angle       5.65916 (  618)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LEU cc_start: 0.6062 (tp) cc_final: 0.5816 (tp)
REVERT: A  395 MET cc_start: 0.6311 (ttt) cc_final: 0.5957 (mmm)
REVERT: D  820 MET cc_start: 0.5956 (mpp) cc_final: 0.5719 (mmt)
REVERT: D  857 ASN cc_start: 0.3671 (p0) cc_final: 0.3023 (p0)
REVERT: C  793 LEU cc_start: 0.5119 (mt) cc_final: 0.4569 (mt)
REVERT: C  802 ASP cc_start: 0.6109 (t0) cc_final: 0.5834 (t0)
REVERT: C  810 TYR cc_start: 0.3241 (m-10) cc_final: 0.2130 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1095
  time to fit residues: 14.5143
Evaluate side-chains
  97 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0370
   chunk 34 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0870
   chunk 3 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.4036

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

Flipped N/Q/H residues before XYZ refinement:
C 805 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.182196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.171924 restraints weight = 9190.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.173324 restraints weight = 6501.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.174516 restraints weight = 4982.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.175168 restraints weight = 3896.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.175736 restraints weight = 3275.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.4313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5729
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3949  Z= 0.134
  Angle     :  0.597   7.108   5307  Z= 0.311
  Chirality :  0.042   0.140    596
  Planarity :  0.004   0.032    708
  Dihedral  :  4.999  21.186    563
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.38), residues: 489
  helix: -0.35 (0.32), residues: 249
  sheet: -2.04 (0.59), residues: 76
  loop : -1.40 (0.50), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 419 
 TYR   0.009   0.001   TYR C 832 
 PHE   0.004   0.001   PHE D 840 
 TRP   0.016   0.002   TRP D 827 
 HIS   0.002   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3947)
  covalent geometry    : angle       0.59694 ( 5303)
  SS BOND              : bond        0.00368 (    2)
  SS BOND              : angle       0.88171 (    4)
  hydrogen bonds       : bond        0.04353 (  209)
  hydrogen bonds       : angle       5.08013 (  618)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  384 ARG cc_start: 0.7298 (mtm180) cc_final: 0.6675 (ttm170)
REVERT: A  395 MET cc_start: 0.6475 (ttt) cc_final: 0.6124 (mmm)
REVERT: D  857 ASN cc_start: 0.3417 (p0) cc_final: 0.2226 (p0)
REVERT: C  793 LEU cc_start: 0.4874 (mt) cc_final: 0.4644 (mt)
REVERT: C  810 TYR cc_start: 0.3772 (m-10) cc_final: 0.2942 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1063
  time to fit residues: 13.4882
Evaluate side-chains
  99 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   chunk 9 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0470
   chunk 16 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0770
   chunk 7 optimal weight:    0.3980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.2836

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

Flipped N/Q/H residues before XYZ refinement:
C 805 ASN
F 105 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.180311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.165801 restraints weight = 8157.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.168549 restraints weight = 5445.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.170522 restraints weight = 3840.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.171933 restraints weight = 2835.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.172903 restraints weight = 2191.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.4271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5704
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3949  Z= 0.115
  Angle     :  0.553   7.552   5307  Z= 0.290
  Chirality :  0.040   0.149    596
  Planarity :  0.003   0.027    708
  Dihedral  :  4.695  19.940    563
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.24 (0.38), residues: 489
  helix: -0.02 (0.32), residues: 251
  sheet: -2.46 (0.61), residues: 72
  loop : -1.02 (0.50), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 419 
 TYR   0.007   0.001   TYR C 832 
 PHE   0.004   0.001   PHE D 840 
 TRP   0.015   0.002   TRP D 827 
 HIS   0.002   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 3947)
  covalent geometry    : angle       0.55284 ( 5303)
  SS BOND              : bond        0.00349 (    2)
  SS BOND              : angle       0.76927 (    4)
  hydrogen bonds       : bond        0.03904 (  209)
  hydrogen bonds       : angle       4.74330 (  618)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  395 MET cc_start: 0.6363 (ttt) cc_final: 0.6061 (mmm)
REVERT: B  386 GLN cc_start: 0.8329 (mm110) cc_final: 0.7718 (mm-40)
REVERT: B  389 ARG cc_start: 0.6193 (ptp90) cc_final: 0.4886 (ptp90)
REVERT: D  817 GLN cc_start: 0.7051 (mm110) cc_final: 0.5820 (mt0)
REVERT: D  820 MET cc_start: 0.6136 (mpp) cc_final: 0.5785 (mmp)
REVERT: D  857 ASN cc_start: 0.3486 (p0) cc_final: 0.2886 (p0)
REVERT: C  793 LEU cc_start: 0.4992 (mt) cc_final: 0.4694 (mt)
REVERT: F  100 GLN cc_start: 0.6695 (pp30) cc_final: 0.6419 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1145
  time to fit residues: 13.9553
Evaluate side-chains
  94 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    0.4980
   chunk 28 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.4325 r_free = 0.4325 target = 0.177627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.162013 restraints weight = 8091.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.165151 restraints weight = 5301.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.167371 restraints weight = 3670.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.168899 restraints weight = 2670.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.169874 restraints weight = 2036.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.4236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5771
moved from start:          0.3774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3949  Z= 0.149
  Angle     :  0.592   7.830   5307  Z= 0.309
  Chirality :  0.042   0.159    596
  Planarity :  0.004   0.057    708
  Dihedral  :  4.931  20.575    563
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  3.23 %
    Favored  : 96.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.38), residues: 489
  helix:  0.04 (0.32), residues: 248
  sheet: -1.96 (0.60), residues: 76
  loop : -1.26 (0.51), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 419 
 TYR   0.011   0.001   TYR C 832 
 PHE   0.006   0.002   PHE D 840 
 TRP   0.018   0.002   TRP C 809 
 HIS   0.004   0.002   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3947)
  covalent geometry    : angle       0.59185 ( 5303)
  SS BOND              : bond        0.00451 (    2)
  SS BOND              : angle       1.00832 (    4)
  hydrogen bonds       : bond        0.03997 (  209)
  hydrogen bonds       : angle       4.84371 (  618)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7689 (ttm-80)
REVERT: A  395 MET cc_start: 0.6325 (ttt) cc_final: 0.6017 (mmm)
REVERT: B  386 GLN cc_start: 0.8350 (mm110) cc_final: 0.7485 (mm-40)
REVERT: B  389 ARG cc_start: 0.6140 (ptp90) cc_final: 0.4871 (ptp90)
REVERT: D  857 ASN cc_start: 0.3513 (p0) cc_final: 0.2957 (p0)
REVERT: C  793 LEU cc_start: 0.5056 (mt) cc_final: 0.4807 (mt)
REVERT: C  829 SER cc_start: 0.8956 (p) cc_final: 0.8744 (p)
REVERT: F  100 GLN cc_start: 0.6688 (pp30) cc_final: 0.6431 (pp30)
  outliers start: 1
  outliers final: 1
  residues processed: 109
  average time/residue: 0.1037
  time to fit residues: 13.1987
Evaluate side-chains
  96 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0000
   chunk 4 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.5784

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.180785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.169889 restraints weight = 9402.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.171627 restraints weight = 6857.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.172625 restraints weight = 5189.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.173590 restraints weight = 4187.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.174138 restraints weight = 3442.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5797
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3949  Z= 0.160
  Angle     :  0.611   7.804   5307  Z= 0.322
  Chirality :  0.043   0.157    596
  Planarity :  0.004   0.051    708
  Dihedral  :  5.152  21.290    563
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.39), residues: 489
  helix:  0.05 (0.32), residues: 245
  sheet: -2.32 (0.63), residues: 65
  loop : -1.10 (0.50), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 419 
 TYR   0.012   0.002   TYR C 832 
 PHE   0.007   0.002   PHE D 840 
 TRP   0.015   0.002   TRP C 809 
 HIS   0.003   0.002   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3947)
  covalent geometry    : angle       0.61077 ( 5303)
  SS BOND              : bond        0.00509 (    2)
  SS BOND              : angle       1.10351 (    4)
  hydrogen bonds       : bond        0.04057 (  209)
  hydrogen bonds       : angle       4.94492 (  618)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7773 (ttm-80)
REVERT: A  395 MET cc_start: 0.6454 (ttt) cc_final: 0.6137 (mmm)
REVERT: A  418 GLU cc_start: 0.8095 (pp20) cc_final: 0.7313 (pp20)
REVERT: B  386 GLN cc_start: 0.8366 (mm110) cc_final: 0.7417 (mm-40)
REVERT: B  389 ARG cc_start: 0.6137 (ptp90) cc_final: 0.4909 (ptp90)
REVERT: D  817 GLN cc_start: 0.7049 (mp-120) cc_final: 0.6121 (mt0)
REVERT: D  820 MET cc_start: 0.6293 (mpp) cc_final: 0.6067 (mmt)
REVERT: D  857 ASN cc_start: 0.3536 (p0) cc_final: 0.2997 (p0)
REVERT: D  878 TRP cc_start: 0.6634 (m100) cc_final: 0.6408 (m100)
REVERT: C  793 LEU cc_start: 0.4966 (mt) cc_final: 0.4458 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0977
  time to fit residues: 11.8695
Evaluate side-chains
  91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 9 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0870
   chunk 7 optimal weight:    0.3980
   chunk 46 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0270
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.2616

-------------------------------------------------------------------------------
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 = 0.4405 r_free = 0.4405 target = 0.184904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.174157 restraints weight = 9432.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.175729 restraints weight = 6826.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.176961 restraints weight = 5205.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.177707 restraints weight = 4132.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.178243 restraints weight = 3437.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.4277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5707
moved from start:          0.4327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   3949  Z= 0.113
  Angle     :  0.576   8.066   5307  Z= 0.299
  Chirality :  0.040   0.131    596
  Planarity :  0.003   0.030    708
  Dihedral  :  4.698  19.452    563
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.39), residues: 489
  helix:  0.32 (0.32), residues: 248
  sheet: -2.08 (0.61), residues: 71
  loop : -1.00 (0.51), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 419 
 TYR   0.009   0.001   TYR C 810 
 PHE   0.004   0.001   PHE D 840 
 TRP   0.016   0.002   TRP C 809 
 HIS   0.001   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 3947)
  covalent geometry    : angle       0.57603 ( 5303)
  SS BOND              : bond        0.00363 (    2)
  SS BOND              : angle       0.81282 (    4)
  hydrogen bonds       : bond        0.03720 (  209)
  hydrogen bonds       : angle       4.53589 (  618)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7672 (ttm-80)
REVERT: A  395 MET cc_start: 0.6130 (ttt) cc_final: 0.5914 (mmm)
REVERT: A  397 GLU cc_start: 0.6983 (pm20) cc_final: 0.6724 (pm20)
REVERT: A  418 GLU cc_start: 0.8002 (pp20) cc_final: 0.7273 (pp20)
REVERT: B  386 GLN cc_start: 0.8372 (mm110) cc_final: 0.7414 (mm110)
REVERT: B  389 ARG cc_start: 0.6183 (ptp90) cc_final: 0.5130 (ptp90)
REVERT: D  802 ASP cc_start: 0.6699 (t0) cc_final: 0.6457 (t0)
REVERT: D  817 GLN cc_start: 0.7079 (mp-120) cc_final: 0.6085 (mt0)
REVERT: D  857 ASN cc_start: 0.3595 (p0) cc_final: 0.3060 (p0)
REVERT: C  793 LEU cc_start: 0.4763 (mt) cc_final: 0.4483 (mt)
REVERT: C  810 TYR cc_start: 0.3232 (m-10) cc_final: 0.2387 (m-80)
REVERT: C  878 TRP cc_start: 0.7018 (m100) cc_final: 0.6775 (m100)
REVERT: F  100 GLN cc_start: 0.6919 (pp30) cc_final: 0.6678 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1055
  time to fit residues: 12.4871
Evaluate side-chains
  92 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 26 optimal weight:    0.2980
   chunk 22 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0000
   chunk 12 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.3984

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

Flipped N/Q/H residues before XYZ refinement:
E 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.182867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.171969 restraints weight = 9313.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.173669 restraints weight = 6574.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.174908 restraints weight = 4905.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.175597 restraints weight = 3807.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.176314 restraints weight = 3177.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5690
moved from start:          0.4418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3949  Z= 0.131
  Angle     :  0.599   8.111   5307  Z= 0.310
  Chirality :  0.041   0.132    596
  Planarity :  0.004   0.032    708
  Dihedral  :  4.791  19.460    563
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  1.00 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.39), residues: 489
  helix:  0.45 (0.33), residues: 248
  sheet: -2.15 (0.60), residues: 71
  loop : -1.05 (0.51), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 403 
 TYR   0.009   0.001   TYR C 832 
 PHE   0.005   0.002   PHE D 840 
 TRP   0.016   0.002   TRP C 809 
 HIS   0.002   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3947)
  covalent geometry    : angle       0.59895 ( 5303)
  SS BOND              : bond        0.00422 (    2)
  SS BOND              : angle       0.91925 (    4)
  hydrogen bonds       : bond        0.03930 (  209)
  hydrogen bonds       : angle       4.63340 (  618)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 ARG cc_start: 0.8166 (ttm-80) cc_final: 0.7709 (ttm-80)
REVERT: A  395 MET cc_start: 0.6241 (ttt) cc_final: 0.6001 (mmm)
REVERT: A  418 GLU cc_start: 0.7861 (pp20) cc_final: 0.7077 (pp20)
REVERT: B  386 GLN cc_start: 0.8170 (mm110) cc_final: 0.7306 (mm110)
REVERT: B  389 ARG cc_start: 0.6224 (ptp90) cc_final: 0.5232 (ptp90)
REVERT: D  802 ASP cc_start: 0.6462 (t0) cc_final: 0.6077 (t0)
REVERT: D  817 GLN cc_start: 0.7078 (mp-120) cc_final: 0.6115 (mt0)
REVERT: D  857 ASN cc_start: 0.2980 (p0) cc_final: 0.2411 (p0)
REVERT: D  878 TRP cc_start: 0.6627 (m100) cc_final: 0.6208 (m100)
REVERT: C  810 TYR cc_start: 0.3495 (m-10) cc_final: 0.2315 (m-80)
REVERT: C  827 TRP cc_start: 0.6098 (m-10) cc_final: 0.4553 (m-90)
REVERT: C  878 TRP cc_start: 0.7012 (m100) cc_final: 0.6760 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1002
  time to fit residues: 12.5354
Evaluate side-chains
  93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 2 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 37 optimal weight:    0.4980
   chunk 8 optimal weight:    0.1980
   overall best weight:    0.5782

-------------------------------------------------------------------------------
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 = 0.4370 r_free = 0.4370 target = 0.180750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.169702 restraints weight = 9379.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.171513 restraints weight = 6643.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.172501 restraints weight = 4901.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.173532 restraints weight = 3925.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.174050 restraints weight = 3171.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5740
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3949  Z= 0.165
  Angle     :  0.657   8.203   5307  Z= 0.342
  Chirality :  0.043   0.162    596
  Planarity :  0.004   0.027    708
  Dihedral  :  5.149  22.523    563
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.39), residues: 489
  helix:  0.24 (0.33), residues: 248
  sheet: -2.25 (0.64), residues: 65
  loop : -1.17 (0.50), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 419 
 TYR   0.012   0.002   TYR C 832 
 PHE   0.007   0.002   PHE D 840 
 TRP   0.020   0.003   TRP C 827 
 HIS   0.002   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3947)
  covalent geometry    : angle       0.65690 ( 5303)
  SS BOND              : bond        0.00518 (    2)
  SS BOND              : angle       1.17459 (    4)
  hydrogen bonds       : bond        0.04048 (  209)
  hydrogen bonds       : angle       4.90655 (  618)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7730 (ttm-80)
REVERT: A  395 MET cc_start: 0.6175 (ttt) cc_final: 0.5892 (mmm)
REVERT: A  418 GLU cc_start: 0.7811 (pp20) cc_final: 0.7126 (pp20)
REVERT: B  386 GLN cc_start: 0.8180 (mm110) cc_final: 0.7306 (mm-40)
REVERT: B  389 ARG cc_start: 0.6239 (ptp90) cc_final: 0.5214 (ptp90)
REVERT: D  802 ASP cc_start: 0.6582 (t0) cc_final: 0.6199 (t0)
REVERT: D  817 GLN cc_start: 0.7116 (mp-120) cc_final: 0.6180 (mt0)
REVERT: D  857 ASN cc_start: 0.2479 (p0) cc_final: 0.2005 (p0)
REVERT: D  878 TRP cc_start: 0.6622 (m100) cc_final: 0.6250 (m100)
REVERT: C  793 LEU cc_start: 0.4589 (mt) cc_final: 0.4276 (mt)
REVERT: C  875 SER cc_start: 0.6672 (t) cc_final: 0.6434 (t)
REVERT: C  878 TRP cc_start: 0.7191 (m100) cc_final: 0.6854 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0963
  time to fit residues: 11.9156
Evaluate side-chains
  95 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 26 optimal weight:    0.0060
   chunk 34 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 11 optimal weight:    0.4980
   chunk 6 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.180504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.169617 restraints weight = 9235.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.171328 restraints weight = 6489.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.172499 restraints weight = 4823.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.173184 restraints weight = 3789.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.173894 restraints weight = 3180.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.4296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5742
moved from start:          0.4471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3949  Z= 0.158
  Angle     :  0.662   8.191   5307  Z= 0.348
  Chirality :  0.044   0.204    596
  Planarity :  0.004   0.030    708
  Dihedral  :  5.117  21.665    563
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.38), residues: 489
  helix:  0.25 (0.32), residues: 246
  sheet: -2.23 (0.63), residues: 65
  loop : -1.27 (0.49), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 419 
 TYR   0.011   0.001   TYR C 832 
 PHE   0.007   0.002   PHE D 840 
 TRP   0.025   0.003   TRP C 827 
 HIS   0.002   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3947)
  covalent geometry    : angle       0.66168 ( 5303)
  SS BOND              : bond        0.00497 (    2)
  SS BOND              : angle       1.12754 (    4)
  hydrogen bonds       : bond        0.04133 (  209)
  hydrogen bonds       : angle       4.97649 (  618)

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

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

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  978 Ramachandran restraints generated.
    489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7754 (ttm-80)
REVERT: A  418 GLU cc_start: 0.7835 (pp20) cc_final: 0.7150 (pp20)
REVERT: B  386 GLN cc_start: 0.8168 (mm110) cc_final: 0.7311 (mm-40)
REVERT: B  389 ARG cc_start: 0.6367 (ptp90) cc_final: 0.5260 (ptp90)
REVERT: D  802 ASP cc_start: 0.6545 (t0) cc_final: 0.6153 (t0)
REVERT: D  817 GLN cc_start: 0.7103 (mp-120) cc_final: 0.6169 (mt0)
REVERT: D  857 ASN cc_start: 0.2475 (p0) cc_final: 0.2135 (p0)
REVERT: D  878 TRP cc_start: 0.6660 (m100) cc_final: 0.6351 (m100)
REVERT: C  793 LEU cc_start: 0.4498 (mt) cc_final: 0.4264 (mt)
REVERT: C  823 VAL cc_start: 0.6327 (p) cc_final: 0.6123 (p)
REVERT: C  875 SER cc_start: 0.6716 (t) cc_final: 0.6513 (t)
REVERT: C  878 TRP cc_start: 0.7175 (m100) cc_final: 0.6830 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1023
  time to fit residues: 12.4011
Evaluate side-chains
  94 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0970
   chunk 40 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   chunk 44 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0970
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.3776

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

Flipped N/Q/H residues before XYZ refinement:
C 805 ASN
F 100 GLN
** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.182316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.171456 restraints weight = 9241.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.173175 restraints weight = 6609.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.174322 restraints weight = 4959.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.174975 restraints weight = 3887.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.175756 restraints weight = 3284.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5698
moved from start:          0.4612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3949  Z= 0.134
  Angle     :  0.653   8.288   5307  Z= 0.341
  Chirality :  0.042   0.180    596
  Planarity :  0.003   0.026    708
  Dihedral  :  4.942  20.869    563
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.25 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.39), residues: 489
  helix:  0.34 (0.33), residues: 247
  sheet: -2.04 (0.65), residues: 65
  loop : -1.27 (0.49), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 419 
 TYR   0.008   0.001   TYR C 832 
 PHE   0.006   0.002   PHE D 840 
 TRP   0.028   0.003   TRP C 827 
 HIS   0.002   0.001   HIS B 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 3947)
  covalent geometry    : angle       0.65256 ( 5303)
  SS BOND              : bond        0.00433 (    2)
  SS BOND              : angle       0.94011 (    4)
  hydrogen bonds       : bond        0.03894 (  209)
  hydrogen bonds       : angle       4.78202 (  618)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 926.87 seconds
wall clock time: 16 minutes 35.28 seconds (995.28 seconds total)