Starting phenix.real_space_refine
on Fri May  9 21:30:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8afl_15401/05_2025/8afl_15401.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8afl_15401/05_2025/8afl_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_15401/05_2025/8afl_15401.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8afl_15401/05_2025/8afl_15401.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8afl_15401/05_2025/8afl_15401.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8afl_15401/05_2025/8afl_15401.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.20, per 1000 atoms: 0.82
  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: 1.02
  Conformation dependent library (CDL) restraints added in 488.7 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: 0.51
  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: 1.03

  Time building geometry restraints manager: 1.18 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:             0.620
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.370
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.200
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.025   0.004   TRP D 827 
 HIS   0.002   0.001   HIS B 406 
 PHE   0.010   0.003   PHE D 840 
 TYR   0.019   0.002   TYR C 872 
 ARG   0.020   0.001   ARG B 380 

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

*********************** 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  : 0.448 
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: 0.3870 (p0) cc_final: 0.3541 (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: 0.2479
  time to fit residues: 29.7824
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  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 36 optimal weight:    0.1980
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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
** F 100 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 = 0.4302 r_free = 0.4302 target = 0.174724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.159216 restraints weight = 7728.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.162167 restraints weight = 5091.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.164096 restraints weight = 3524.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5904
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3949  Z= 0.202
  Angle     :  0.703   9.057   5307  Z= 0.370
  Chirality :  0.045   0.153    596
  Planarity :  0.005   0.042    708
  Dihedral  :  5.781  24.535    563
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  6.22 %
    Favored  : 93.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.36), residues: 489
  helix: -1.18 (0.31), residues: 249
  sheet: -2.77 (0.75), residues: 46
  loop : -1.61 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP C 809 
 HIS   0.003   0.002   HIS B 406 
 PHE   0.008   0.002   PHE D 840 
 TYR   0.015   0.002   TYR C 872 
 ARG   0.005   0.001   ARG F 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05421 (  209)
  hydrogen bonds       : angle       6.15106 (  618)
  SS BOND              : bond        0.00570 (    2)
  SS BOND              : angle       1.44150 (    4)
  covalent geometry    : bond        0.00418 ( 3947)
  covalent geometry    : angle       0.70240 ( 5303)

*********************** 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
  113 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LEU cc_start: 0.6299 (tp) cc_final: 0.6029 (tp)
REVERT: A  395 MET cc_start: 0.6372 (ttt) cc_final: 0.6028 (mmm)
REVERT: B  395 MET cc_start: 0.7575 (ttt) cc_final: 0.7342 (ttt)
REVERT: B  401 GLN cc_start: 0.7448 (tp-100) cc_final: 0.6882 (tp-100)
REVERT: D  802 ASP cc_start: 0.6938 (t0) cc_final: 0.6720 (t0)
REVERT: D  820 MET cc_start: 0.6519 (mpp) cc_final: 0.6151 (mmt)
REVERT: D  857 ASN cc_start: 0.4140 (p0) cc_final: 0.3767 (p0)
REVERT: C  793 LEU cc_start: 0.5519 (mt) cc_final: 0.4782 (mt)
REVERT: C  802 ASP cc_start: 0.7431 (t0) cc_final: 0.7071 (t0)
REVERT: C  825 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7895 (p)
REVERT: C  861 GLU cc_start: 0.7290 (tm-30) cc_final: 0.7026 (tm-30)
REVERT: E  114 ARG cc_start: 0.6978 (ptp90) cc_final: 0.6720 (ptp-170)
REVERT: E  144 ASP cc_start: 0.6240 (m-30) cc_final: 0.6010 (m-30)
REVERT: F  124 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7536 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2527
  time to fit residues: 32.9700
Evaluate side-chains
  101 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 10 optimal weight:    0.4980
   chunk 24 optimal weight:    0.0970
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 23 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.4374 r_free = 0.4374 target = 0.181177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.170768 restraints weight = 9131.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.172369 restraints weight = 6453.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.173498 restraints weight = 4806.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5814
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3949  Z= 0.145
  Angle     :  0.614   7.624   5307  Z= 0.320
  Chirality :  0.042   0.146    596
  Planarity :  0.004   0.037    708
  Dihedral  :  5.268  21.874    563
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.37), residues: 489
  helix: -0.56 (0.32), residues: 247
  sheet: -1.98 (0.62), residues: 69
  loop : -1.53 (0.49), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 827 
 HIS   0.002   0.001   HIS B 406 
 PHE   0.005   0.002   PHE D 840 
 TYR   0.012   0.001   TYR D  13 
 ARG   0.008   0.001   ARG A 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04503 (  209)
  hydrogen bonds       : angle       5.30258 (  618)
  SS BOND              : bond        0.00450 (    2)
  SS BOND              : angle       0.94345 (    4)
  covalent geometry    : bond        0.00293 ( 3947)
  covalent geometry    : angle       0.61379 ( 5303)

*********************** 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
  113 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  395 MET cc_start: 0.6463 (ttt) cc_final: 0.6178 (mmm)
REVERT: B  401 GLN cc_start: 0.7390 (tp-100) cc_final: 0.6905 (tp-100)
REVERT: D  820 MET cc_start: 0.6477 (mpp) cc_final: 0.6053 (mmt)
REVERT: D  857 ASN cc_start: 0.3990 (p0) cc_final: 0.2915 (p0)
REVERT: C  793 LEU cc_start: 0.5251 (mt) cc_final: 0.4881 (mt)
REVERT: C  794 SER cc_start: 0.6581 (p) cc_final: 0.6304 (p)
REVERT: C  802 ASP cc_start: 0.6974 (t0) cc_final: 0.6716 (t0)
REVERT: E  144 ASP cc_start: 0.6294 (m-30) cc_final: 0.6085 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2438
  time to fit residues: 31.6546
Evaluate side-chains
  100 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 17 optimal weight:    0.3980
   chunk 43 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.179662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.169115 restraints weight = 9134.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.170658 restraints weight = 6575.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.171778 restraints weight = 4976.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5855
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3949  Z= 0.172
  Angle     :  0.629   7.179   5307  Z= 0.330
  Chirality :  0.043   0.151    596
  Planarity :  0.004   0.059    708
  Dihedral  :  5.402  23.195    563
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.37), residues: 489
  helix: -0.56 (0.31), residues: 250
  sheet: -2.89 (0.70), residues: 46
  loop : -1.58 (0.46), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP C 809 
 HIS   0.003   0.002   HIS B 406 
 PHE   0.009   0.002   PHE D 840 
 TYR   0.011   0.002   TYR C 832 
 ARG   0.004   0.000   ARG B 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04260 (  209)
  hydrogen bonds       : angle       5.30906 (  618)
  SS BOND              : bond        0.00525 (    2)
  SS BOND              : angle       1.22198 (    4)
  covalent geometry    : bond        0.00357 ( 3947)
  covalent geometry    : angle       0.62884 ( 5303)

*********************** 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
  105 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8103 (mm110)
REVERT: B  389 ARG cc_start: 0.6281 (ptp90) cc_final: 0.4771 (ptp90)
REVERT: D  820 MET cc_start: 0.6656 (mpp) cc_final: 0.6177 (mmt)
REVERT: D  857 ASN cc_start: 0.3793 (p0) cc_final: 0.3314 (p0)
REVERT: D  878 TRP cc_start: 0.6717 (m100) cc_final: 0.6514 (m100)
REVERT: C  793 LEU cc_start: 0.5317 (mt) cc_final: 0.4926 (mt)
REVERT: C  802 ASP cc_start: 0.7184 (t0) cc_final: 0.6854 (t0)
REVERT: C  861 GLU cc_start: 0.7250 (tm-30) cc_final: 0.7025 (tm-30)
REVERT: F  100 GLN cc_start: 0.6705 (pp30) cc_final: 0.6434 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.2142
  time to fit residues: 26.3320
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  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0570
   chunk 30 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.4368 r_free = 0.4368 target = 0.180977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.169987 restraints weight = 9452.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.171692 restraints weight = 6776.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.172874 restraints weight = 5095.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.4218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5836
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3949  Z= 0.159
  Angle     :  0.625   7.490   5307  Z= 0.324
  Chirality :  0.043   0.153    596
  Planarity :  0.004   0.047    708
  Dihedral  :  5.316  22.394    563
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.49 %
    Favored  : 97.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.38), residues: 489
  helix: -0.43 (0.32), residues: 251
  sheet: -2.45 (0.64), residues: 59
  loop : -1.59 (0.48), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 827 
 HIS   0.003   0.002   HIS B 406 
 PHE   0.007   0.002   PHE D 840 
 TYR   0.010   0.001   TYR C 832 
 ARG   0.006   0.001   ARG B 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04155 (  209)
  hydrogen bonds       : angle       5.12737 (  618)
  SS BOND              : bond        0.00525 (    2)
  SS BOND              : angle       1.15358 (    4)
  covalent geometry    : bond        0.00334 ( 3947)
  covalent geometry    : angle       0.62477 ( 5303)

*********************** 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
  112 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: A  395 MET cc_start: 0.6567 (ttt) cc_final: 0.6115 (mmm)
REVERT: B  386 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7952 (mm110)
REVERT: B  389 ARG cc_start: 0.6376 (ptp90) cc_final: 0.4862 (ptp90)
REVERT: B  397 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6686 (mm-30)
REVERT: D  817 GLN cc_start: 0.7166 (mp-120) cc_final: 0.6179 (mt0)
REVERT: D  820 MET cc_start: 0.6635 (mpp) cc_final: 0.6127 (mmt)
REVERT: D  857 ASN cc_start: 0.3545 (p0) cc_final: 0.3041 (p0)
REVERT: D  878 TRP cc_start: 0.6683 (m100) cc_final: 0.6456 (m100)
REVERT: C  793 LEU cc_start: 0.5074 (mt) cc_final: 0.4814 (mt)
REVERT: C  802 ASP cc_start: 0.6867 (t0) cc_final: 0.6521 (t0)
REVERT: C  861 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6983 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 112
  average time/residue: 0.2177
  time to fit residues: 28.4810
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  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 5 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0970
   chunk 33 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0670
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.2916

-------------------------------------------------------------------------------
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 = 0.4411 r_free = 0.4411 target = 0.184714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.173790 restraints weight = 9247.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.175456 restraints weight = 6726.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.176437 restraints weight = 5144.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5716
moved from start:          0.4287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3949  Z= 0.118
  Angle     :  0.574   8.076   5307  Z= 0.300
  Chirality :  0.040   0.154    596
  Planarity :  0.003   0.029    708
  Dihedral  :  4.834  20.275    563
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.39), residues: 489
  helix: -0.02 (0.32), residues: 245
  sheet: -2.59 (0.59), residues: 73
  loop : -1.01 (0.51), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 809 
 HIS   0.001   0.001   HIS B 406 
 PHE   0.006   0.002   PHE D 840 
 TYR   0.009   0.001   TYR C 872 
 ARG   0.007   0.000   ARG B 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03854 (  209)
  hydrogen bonds       : angle       4.70537 (  618)
  SS BOND              : bond        0.00389 (    2)
  SS BOND              : angle       0.82838 (    4)
  covalent geometry    : bond        0.00243 ( 3947)
  covalent geometry    : angle       0.57353 ( 5303)

*********************** 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
  109 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  384 ARG cc_start: 0.7707 (ttm-80) cc_final: 0.7497 (ttp-110)
REVERT: B  386 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7714 (mm-40)
REVERT: B  389 ARG cc_start: 0.6223 (ptp90) cc_final: 0.4776 (ptp90)
REVERT: D  817 GLN cc_start: 0.7226 (mp-120) cc_final: 0.6146 (mt0)
REVERT: D  820 MET cc_start: 0.6008 (mpp) cc_final: 0.5718 (mmt)
REVERT: D  857 ASN cc_start: 0.3451 (p0) cc_final: 0.3034 (p0)
REVERT: D  878 TRP cc_start: 0.6560 (m100) cc_final: 0.6252 (m100)
REVERT: C  793 LEU cc_start: 0.4562 (mt) cc_final: 0.4278 (mt)
REVERT: C  810 TYR cc_start: 0.3205 (m-10) cc_final: 0.2174 (m-80)
REVERT: C  875 SER cc_start: 0.6098 (t) cc_final: 0.5797 (t)
REVERT: C  878 TRP cc_start: 0.6889 (m100) cc_final: 0.6541 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.2308
  time to fit residues: 29.2656
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  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0870
   chunk 15 optimal weight:    0.1980
   chunk 2 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 21 optimal weight:    0.2980
   chunk 1 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 46 optimal weight:    0.1980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.2758

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

Flipped N/Q/H residues before XYZ refinement:
C 805 ASN
E 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.185237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.174130 restraints weight = 9251.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.175859 restraints weight = 6727.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.176938 restraints weight = 5115.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5703
moved from start:          0.4483

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     :  0.560   8.058   5307  Z= 0.291
  Chirality :  0.040   0.135    596
  Planarity :  0.003   0.030    708
  Dihedral  :  4.684  19.316    563
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  1.24 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.39), residues: 489
  helix:  0.30 (0.33), residues: 245
  sheet: -2.03 (0.65), residues: 65
  loop : -1.09 (0.50), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 827 
 HIS   0.001   0.001   HIS B 406 
 PHE   0.006   0.002   PHE D 840 
 TYR   0.007   0.001   TYR C 832 
 ARG   0.007   0.000   ARG B 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03698 (  209)
  hydrogen bonds       : angle       4.51375 (  618)
  SS BOND              : bond        0.00355 (    2)
  SS BOND              : angle       0.78040 (    4)
  covalent geometry    : bond        0.00231 ( 3947)
  covalent geometry    : angle       0.55981 ( 5303)

*********************** 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
  105 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7707 (mm-40)
REVERT: B  389 ARG cc_start: 0.6239 (ptp90) cc_final: 0.4910 (ptp90)
REVERT: D  817 GLN cc_start: 0.7189 (mp-120) cc_final: 0.6104 (mt0)
REVERT: D  857 ASN cc_start: 0.3101 (p0) cc_final: 0.2519 (p0)
REVERT: D  878 TRP cc_start: 0.6560 (m100) cc_final: 0.6139 (m100)
REVERT: C  875 SER cc_start: 0.6437 (t) cc_final: 0.6043 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.2327
  time to fit residues: 28.8166
Evaluate side-chains
  90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 19 optimal weight:    0.0670
   chunk 33 optimal weight:    0.3980
   chunk 35 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0870
   chunk 29 optimal weight:    0.8980
   chunk 16 optimal weight:    0.1980
   chunk 25 optimal weight:    0.4980
   chunk 9 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.2496

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.184731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.174151 restraints weight = 9234.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.175831 restraints weight = 6633.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.176779 restraints weight = 4950.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.4328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5667
moved from start:          0.4709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   3949  Z= 0.116
  Angle     :  0.581   8.206   5307  Z= 0.302
  Chirality :  0.040   0.132    596
  Planarity :  0.003   0.034    708
  Dihedral  :  4.646  19.045    563
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.39), residues: 489
  helix:  0.53 (0.33), residues: 245
  sheet: -1.92 (0.65), residues: 65
  loop : -1.06 (0.50), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP C 827 
 HIS   0.002   0.001   HIS B 406 
 PHE   0.006   0.001   PHE D 840 
 TYR   0.007   0.001   TYR C 832 
 ARG   0.007   0.000   ARG B 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03837 (  209)
  hydrogen bonds       : angle       4.45087 (  618)
  SS BOND              : bond        0.00268 (    2)
  SS BOND              : angle       0.71359 (    4)
  covalent geometry    : bond        0.00238 ( 3947)
  covalent geometry    : angle       0.58102 ( 5303)

*********************** 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
  106 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7729 (mm-40)
REVERT: B  389 ARG cc_start: 0.6314 (ptp90) cc_final: 0.4863 (ptp90)
REVERT: D  817 GLN cc_start: 0.7189 (mp-120) cc_final: 0.6150 (mt0)
REVERT: D  857 ASN cc_start: 0.3103 (p0) cc_final: 0.2876 (p0)
REVERT: D  878 TRP cc_start: 0.6528 (m100) cc_final: 0.6140 (m100)
REVERT: C  878 TRP cc_start: 0.6589 (m100) cc_final: 0.6244 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2172
  time to fit residues: 26.8875
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  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 11 optimal weight:    0.0970
   chunk 40 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0670
   chunk 22 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0020
   chunk 2 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 28 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.2524

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.185856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.175047 restraints weight = 9296.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.176750 restraints weight = 6592.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.177792 restraints weight = 4922.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5643
moved from start:          0.4870

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= 0.116
  Angle     :  0.601   8.224   5307  Z= 0.311
  Chirality :  0.041   0.209    596
  Planarity :  0.004   0.034    708
  Dihedral  :  4.550  17.809    563
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.39), residues: 489
  helix:  0.54 (0.33), residues: 248
  sheet: -1.91 (0.65), residues: 67
  loop : -1.02 (0.51), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP C 827 
 HIS   0.002   0.001   HIS B 406 
 PHE   0.006   0.002   PHE D 840 
 TYR   0.007   0.001   TYR C 832 
 ARG   0.007   0.001   ARG B 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03728 (  209)
  hydrogen bonds       : angle       4.38847 (  618)
  SS BOND              : bond        0.00262 (    2)
  SS BOND              : angle       0.61048 (    4)
  covalent geometry    : bond        0.00240 ( 3947)
  covalent geometry    : angle       0.60111 ( 5303)

*********************** 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
  109 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  817 GLN cc_start: 0.7187 (mp-120) cc_final: 0.6165 (mt0)
REVERT: D  878 TRP cc_start: 0.6525 (m100) cc_final: 0.6137 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.2299
  time to fit residues: 29.3884
Evaluate side-chains
  98 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 15 optimal weight:    0.1980
   chunk 24 optimal weight:    0.4980
   chunk 39 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 44 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0670
   chunk 37 optimal weight:    0.0270
   chunk 18 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.2176

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

Flipped N/Q/H residues before XYZ refinement:
C 805 ASN
E 100 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.185145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.174281 restraints weight = 9441.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.175932 restraints weight = 6753.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.176977 restraints weight = 5079.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5650
moved from start:          0.5155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   3949  Z= 0.117
  Angle     :  0.610   8.154   5307  Z= 0.317
  Chirality :  0.041   0.194    596
  Planarity :  0.003   0.032    708
  Dihedral  :  4.351  16.395    563
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.50 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.39), residues: 489
  helix:  0.67 (0.33), residues: 248
  sheet: -1.64 (0.66), residues: 61
  loop : -1.13 (0.49), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP C 827 
 HIS   0.001   0.001   HIS B 406 
 PHE   0.005   0.002   PHE D 840 
 TYR   0.015   0.001   TYR D 872 
 ARG   0.007   0.000   ARG B 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03741 (  209)
  hydrogen bonds       : angle       4.35829 (  618)
  SS BOND              : bond        0.00191 (    2)
  SS BOND              : angle       0.42428 (    4)
  covalent geometry    : bond        0.00243 ( 3947)
  covalent geometry    : angle       0.61012 ( 5303)

********************** 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
  103 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  817 GLN cc_start: 0.7195 (mp-120) cc_final: 0.6179 (mt0)
REVERT: D  878 TRP cc_start: 0.6496 (m100) cc_final: 0.6140 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 0.2290
  time to fit residues: 27.5507
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  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 27 optimal weight:    0.2980
   chunk 23 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C 805 ASN
E 100 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.181415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.170403 restraints weight = 9084.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.172158 restraints weight = 6546.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.173210 restraints weight = 4931.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.4281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5773
moved from start:          0.4953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3949  Z= 0.163
  Angle     :  0.650   8.190   5307  Z= 0.341
  Chirality :  0.042   0.167    596
  Planarity :  0.004   0.031    708
  Dihedral  :  4.822  19.917    563
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.39), residues: 489
  helix:  0.49 (0.33), residues: 247
  sheet: -2.03 (0.56), residues: 77
  loop : -1.08 (0.53), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP C 827 
 HIS   0.003   0.002   HIS B 406 
 PHE   0.008   0.002   PHE D 840 
 TYR   0.018   0.002   TYR D 872 
 ARG   0.005   0.001   ARG B 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04014 (  209)
  hydrogen bonds       : angle       4.69584 (  618)
  SS BOND              : bond        0.00342 (    2)
  SS BOND              : angle       0.67389 (    4)
  covalent geometry    : bond        0.00345 ( 3947)
  covalent geometry    : angle       0.64950 ( 5303)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1820.47 seconds
wall clock time: 32 minutes 30.09 seconds (1950.09 seconds total)