Starting phenix.real_space_refine
on Wed Feb  4 01:15:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w6c_37320/02_2026/8w6c_37320.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w6c_37320/02_2026/8w6c_37320.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w6c_37320/02_2026/8w6c_37320.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w6c_37320/02_2026/8w6c_37320.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w6c_37320/02_2026/8w6c_37320.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w6c_37320/02_2026/8w6c_37320.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      58      5.16       5
     Na      4      4.78       5
     C    5594      2.51       5
     N    1290      2.21       5
     O    1412      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8360
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 530, 4081
          Classifications: {'peptide': 530}
          Link IDs: {'PTRANS': 33, 'TRANS': 496}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 530, 4081
          Classifications: {'peptide': 530}
          Link IDs: {'PTRANS': 33, 'TRANS': 496}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 133
          Unusual residues: {' NA': 2, '3PH': 1, 'CIT': 1, 'Y01': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 63
          Unusual residues: {' NA': 2, '3PH': 1, 'CIT': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 1.54, per 1000 atoms: 0.18
  Number of scatterers: 8360
  At special positions: 0
  Unit cell: (96.743, 107.613, 90.221, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      58     16.00
     P       2     15.00
     Na      4     11.00
     O    1412      8.00
     N    1290      7.00
     C    5594      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 380.1 milliseconds
  

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1988

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 0 sheets defined
      76.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 4.007A  pdb=" N   GLN A   6 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA A   7 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 24
      Proline residue:  A  21  - end of helix
    Processing helix  chain 'A' and resid 25 through 31
    Processing helix  chain 'A' and resid 33 through 51
      removed outlier: 3.588A  pdb=" N   ALA A  41 " --> pdb=" O   TYR A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 60
    Processing helix  chain 'A' and resid 61 through 67
      removed outlier: 3.970A  pdb=" N   ILE A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 80
      removed outlier: 3.580A  pdb=" N   VAL A  80 " --> pdb=" O   SER A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 103
      removed outlier: 3.673A  pdb=" N   ALA A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   TRP A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 118
      removed outlier: 3.848A  pdb=" N   ARG A 108 " --> pdb=" O   ASN A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 137
    Processing helix  chain 'A' and resid 140 through 163
      Proline residue:  A 150  - end of helix
      removed outlier: 3.708A  pdb=" N   GLN A 163 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 233
      removed outlier: 3.853A  pdb=" N   GLN A 219 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER A 222 " --> pdb=" O   THR A 218 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER A 230 " --> pdb=" O   CYS A 226 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLY A 233 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 254
      removed outlier: 3.970A  pdb=" N   LEU A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN A 247 " --> pdb=" O   ASN A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 290
      Proline residue:  A 272  - end of helix
    Processing helix  chain 'A' and resid 304 through 321
    Processing helix  chain 'A' and resid 326 through 345
    Processing helix  chain 'A' and resid 353 through 358
    Processing helix  chain 'A' and resid 369 through 381
    Processing helix  chain 'A' and resid 409 through 417
    Processing helix  chain 'A' and resid 418 through 438
      removed outlier: 3.591A  pdb=" N   VAL A 422 " --> pdb=" O   PRO A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 446
    Processing helix  chain 'A' and resid 447 through 453
      Proline residue:  A 450  - end of helix
      removed outlier: 4.117A  pdb=" N   SER A 453 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 447 through 453'
    Processing helix  chain 'A' and resid 455 through 471
      removed outlier: 3.723A  pdb=" N   ALA A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ILE A 461 " --> pdb=" O   PRO A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 494
      Proline residue:  A 485  - end of helix
      removed outlier: 3.515A  pdb=" N   SER A 489 " --> pdb=" O   PRO A 485 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ILE A 494 " --> pdb=" O   MET A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 509
      removed outlier: 3.569A  pdb=" N   CYS A 505 " --> pdb=" O   VAL A 501 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   THR A 509 " --> pdb=" O   CYS A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 525
      removed outlier: 3.595A  pdb=" N   ALA A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL A 525 " --> pdb=" O   PRO A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 557
      removed outlier: 4.688A  pdb=" N   LEU A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU A 543 " --> pdb=" O   ALA A 539 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ILE A 545 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASN A 556 " --> pdb=" O   ALA A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 564
    Processing helix  chain 'A' and resid 569 through 573
      removed outlier: 3.579A  pdb=" N   GLN A 573 " --> pdb=" O   SER A 570 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 11
      removed outlier: 4.007A  pdb=" N   GLN B   6 " --> pdb=" O   ALA B   2 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA B   7 " --> pdb=" O   THR B   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 24
      Proline residue:  B  21  - end of helix
    Processing helix  chain 'B' and resid 25 through 31
    Processing helix  chain 'B' and resid 33 through 51
      removed outlier: 3.589A  pdb=" N   ALA B  41 " --> pdb=" O   TYR B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 60
    Processing helix  chain 'B' and resid 61 through 67
      removed outlier: 3.971A  pdb=" N   ILE B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 80
      removed outlier: 3.580A  pdb=" N   VAL B  80 " --> pdb=" O   SER B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 103
      removed outlier: 3.672A  pdb=" N   ALA B  99 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TRP B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 118
      removed outlier: 3.848A  pdb=" N   ARG B 108 " --> pdb=" O   ASN B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 137
    Processing helix  chain 'B' and resid 140 through 163
      Proline residue:  B 150  - end of helix
      removed outlier: 3.708A  pdb=" N   GLN B 163 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 233
      removed outlier: 3.854A  pdb=" N   GLN B 219 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER B 222 " --> pdb=" O   THR B 218 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   SER B 230 " --> pdb=" O   CYS B 226 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLY B 233 " --> pdb=" O   ALA B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 254
      removed outlier: 3.968A  pdb=" N   LEU B 244 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN B 247 " --> pdb=" O   ASN B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 290
      Proline residue:  B 272  - end of helix
    Processing helix  chain 'B' and resid 304 through 321
    Processing helix  chain 'B' and resid 326 through 345
    Processing helix  chain 'B' and resid 353 through 358
    Processing helix  chain 'B' and resid 369 through 381
    Processing helix  chain 'B' and resid 409 through 417
    Processing helix  chain 'B' and resid 418 through 438
      removed outlier: 3.590A  pdb=" N   VAL B 422 " --> pdb=" O   PRO B 418 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 446
    Processing helix  chain 'B' and resid 447 through 453
      Proline residue:  B 450  - end of helix
      removed outlier: 4.117A  pdb=" N   SER B 453 " --> pdb=" O   PRO B 450 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 447 through 453'
    Processing helix  chain 'B' and resid 455 through 471
      removed outlier: 3.723A  pdb=" N   ALA B 460 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE B 461 " --> pdb=" O   PRO B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 494
      Proline residue:  B 485  - end of helix
      removed outlier: 3.516A  pdb=" N   SER B 489 " --> pdb=" O   PRO B 485 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE B 494 " --> pdb=" O   MET B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 509
      removed outlier: 3.570A  pdb=" N   CYS B 505 " --> pdb=" O   VAL B 501 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   THR B 509 " --> pdb=" O   CYS B 505 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 525
      removed outlier: 3.596A  pdb=" N   ALA B 523 " --> pdb=" O   THR B 519 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL B 525 " --> pdb=" O   PRO B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 557
      removed outlier: 4.688A  pdb=" N   LEU B 542 " --> pdb=" O   ARG B 538 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU B 543 " --> pdb=" O   ALA B 539 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ILE B 545 " --> pdb=" O   PHE B 541 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN B 556 " --> pdb=" O   ALA B 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 564
    Processing helix  chain 'B' and resid 569 through 573
      removed outlier: 3.579A  pdb=" N   GLN B 573 " --> pdb=" O   SER B 570 " (cutoff:3.500A)

    487 hydrogen bonds defined for protein.
    1455 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: 1.10

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1267
        1.32 -     1.44: 2253
        1.44 -     1.56: 4966
        1.56 -     1.69: 2
        1.69 -     1.81: 96
  Bond restraints: 8584
  Sorted by residual:
  bond pdb=" O11 3PH A 806 "
       pdb=" P   3PH A 806 "
    ideal  model  delta    sigma   weight residual
    1.703  1.606  0.097 2.00e-02 2.50e+03 2.36e+01
  bond pdb=" O11 3PH B1101 "
       pdb=" P   3PH B1101 "
    ideal  model  delta    sigma   weight residual
    1.703  1.608  0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" C1  3PH A 806 "
       pdb=" O11 3PH A 806 "
    ideal  model  delta    sigma   weight residual
    1.385  1.453 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" C1  3PH B1101 "
       pdb=" O11 3PH B1101 "
    ideal  model  delta    sigma   weight residual
    1.385  1.452 -0.067 2.00e-02 2.50e+03 1.12e+01
  bond pdb=" C   PHE A 359 "
       pdb=" N   PRO A 360 "
    ideal  model  delta    sigma   weight residual
    1.329  1.365 -0.036 1.22e-02 6.72e+03 8.51e+00
  ... (remaining 8579 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 11263
        2.30 -     4.59: 363
        4.59 -     6.89: 72
        6.89 -     9.18: 20
        9.18 -    11.48: 6
  Bond angle restraints: 11724
  Sorted by residual:
  angle pdb=" C   GLU A 396 "
        pdb=" N   ASN A 397 "
        pdb=" CA  ASN A 397 "
      ideal   model   delta    sigma   weight residual
     121.80  131.71   -9.91 2.44e+00 1.68e-01 1.65e+01
  angle pdb=" C   GLU B 396 "
        pdb=" N   ASN B 397 "
        pdb=" CA  ASN B 397 "
      ideal   model   delta    sigma   weight residual
     121.80  131.63   -9.83 2.44e+00 1.68e-01 1.62e+01
  angle pdb=" C   LEU A  61 "
        pdb=" N   PHE A  62 "
        pdb=" CA  PHE A  62 "
      ideal   model   delta    sigma   weight residual
     120.06  124.85   -4.79 1.19e+00 7.06e-01 1.62e+01
  angle pdb=" C   LEU B  61 "
        pdb=" N   PHE B  62 "
        pdb=" CA  PHE B  62 "
      ideal   model   delta    sigma   weight residual
     120.06  124.84   -4.78 1.19e+00 7.06e-01 1.61e+01
  angle pdb=" C   GLU A 302 "
        pdb=" N   LYS A 303 "
        pdb=" CA  LYS A 303 "
      ideal   model   delta    sigma   weight residual
     125.66  131.99   -6.33 1.85e+00 2.92e-01 1.17e+01
  ... (remaining 11719 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.64: 4989
       30.64 -    61.28: 133
       61.28 -    91.93: 14
       91.93 -   122.57: 0
      122.57 -   153.21: 2
  Dihedral angle restraints: 5138
    sinusoidal: 2076
      harmonic: 3062
  Sorted by residual:
  dihedral pdb=" C21 3PH A 806 "
           pdb=" C2  3PH A 806 "
           pdb=" O21 3PH A 806 "
           pdb=" C3  3PH A 806 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.58  -59.21 -153.21     1      3.00e+01 1.11e-03 2.02e+01
  dihedral pdb=" C21 3PH B1101 "
           pdb=" C2  3PH B1101 "
           pdb=" O21 3PH B1101 "
           pdb=" C3  3PH B1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.58  -64.65 -147.77     1      3.00e+01 1.11e-03 1.97e+01
  dihedral pdb=" CA  LYS B 400 "
           pdb=" C   LYS B 400 "
           pdb=" N   LEU B 401 "
           pdb=" CA  LEU B 401 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.21   19.79     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 5135 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 865
       0.044 -    0.088: 382
       0.088 -    0.132: 110
       0.132 -    0.176: 27
       0.176 -    0.220: 10
  Chirality restraints: 1394
  Sorted by residual:
  chirality pdb=" CB  VAL A  73 "
            pdb=" CA  VAL A  73 "
            pdb=" CG1 VAL A  73 "
            pdb=" CG2 VAL A  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CB  VAL B  73 "
            pdb=" CA  VAL B  73 "
            pdb=" CG1 VAL B  73 "
            pdb=" CG2 VAL B  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  VAL A 454 "
            pdb=" N   VAL A 454 "
            pdb=" C   VAL A 454 "
            pdb=" CB  VAL A 454 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1391 not shown)

  Planarity restraints: 1414
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  25 "   -0.052 5.00e-02 4.00e+02   7.71e-02 9.50e+00
        pdb=" N   PRO A  26 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A  26 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A  26 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  25 "    0.051 5.00e-02 4.00e+02   7.68e-02 9.44e+00
        pdb=" N   PRO B  26 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO B  26 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B  26 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 519 "   -0.050 5.00e-02 4.00e+02   7.59e-02 9.22e+00
        pdb=" N   PRO A 520 "    0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 520 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 520 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 1411 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 273
        2.71 -     3.26: 7857
        3.26 -     3.81: 13065
        3.81 -     4.35: 17801
        4.35 -     4.90: 29368
  Nonbonded interactions: 68364
  Sorted by model distance:
  nonbonded pdb=" O1  CIT B1104 "
            pdb=" O7  CIT B1104 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O3  CIT A 804 "
            pdb=" O7  CIT A 804 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" OG  SER B 140 "
            pdb=" O6  CIT B1104 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OG  SER A 140 "
            pdb=" O6  CIT A 804 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   GLN B 158 "
            pdb=" OG  SER B 162 "
     model   vdw
     2.302 3.040
  ... (remaining 68359 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 578 or resid 802 or resid 804))
  selection = (chain 'B' and (resid 1 through 578 or resid 1102 or resid 1104))
}

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 individual isotropic
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:             0.960
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.090
  Find NCS groups from input model:        0.270
  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:6.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
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      :  0.007   0.097   8584  Z= 0.295
  Angle     :  1.049  11.479  11724  Z= 0.560
  Chirality :  0.055   0.220   1394
  Planarity :  0.009   0.077   1414
  Dihedral  : 14.780 153.210   3150
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  4.76 %
    Favored  : 94.10 %
  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: -3.18 (0.21), residues: 1052
  helix: -1.80 (0.15), residues: 756
  sheet:  None (None), residues: 0
  loop : -2.47 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 108 
 TYR   0.008   0.002   TYR A 500 
 PHE   0.022   0.002   PHE A 359 
 TRP   0.028   0.002   TRP B 410 
 HIS   0.006   0.001   HIS B 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00669 ( 8584)
  covalent geometry    : angle       1.04948 (11724)
  hydrogen bonds       : bond        0.16915 (  487)
  hydrogen bonds       : angle       6.24429 ( 1455)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.8573 (mtp) cc_final: 0.8329 (mtm)
REVERT: A  129 MET cc_start: 0.9117 (mtp) cc_final: 0.8600 (mtp)
REVERT: A  286 GLN cc_start: 0.8403 (tt0) cc_final: 0.8157 (tt0)
REVERT: A  295 ARG cc_start: 0.7066 (mtp-110) cc_final: 0.6582 (mpt180)
REVERT: A  320 ARG cc_start: 0.7362 (ttm110) cc_final: 0.7087 (ttp-170)
REVERT: A  433 LYS cc_start: 0.8507 (tptt) cc_final: 0.8199 (tptm)
REVERT: A  514 MET cc_start: 0.8702 (mtm) cc_final: 0.8409 (mtm)
REVERT: B   69 MET cc_start: 0.8619 (mtp) cc_final: 0.8368 (mtm)
REVERT: B  129 MET cc_start: 0.9128 (mtp) cc_final: 0.8595 (mtp)
REVERT: B  295 ARG cc_start: 0.7078 (mtp-110) cc_final: 0.6642 (mpt180)
REVERT: B  433 LYS cc_start: 0.8500 (tptt) cc_final: 0.8181 (tptp)
REVERT: B  514 MET cc_start: 0.8705 (mtm) cc_final: 0.8407 (mtm)
  outliers start: 10
  outliers final: 2
  residues processed: 143
  average time/residue: 0.4897
  time to fit residues: 74.4670
Evaluate side-chains
  112 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 110
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain B residue  240 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A 257 ASN
A 297 ASN
A 308 GLN
A 356 ASN
A 414 ASN
A 556 ASN
B   6 GLN
B 257 ASN
B 286 GLN
B 297 ASN
B 308 GLN
B 356 ASN
B 414 ASN
B 556 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.125777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.101454 restraints weight = 9040.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 1.37
r_work: 0.2921 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8584  Z= 0.138
  Angle     :  0.664   7.450  11724  Z= 0.320
  Chirality :  0.042   0.153   1394
  Planarity :  0.007   0.057   1414
  Dihedral  : 10.594 153.990   1334
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  :  9.07 %
    Favored  : 88.44 %
  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: -0.62 (0.26), residues: 1052
  helix:  0.34 (0.19), residues: 758
  sheet:  None (None), residues: 0
  loop : -2.30 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 346 
 TYR   0.007   0.001   TYR B 500 
 PHE   0.013   0.001   PHE B 351 
 TRP   0.019   0.002   TRP A 410 
 HIS   0.002   0.001   HIS B 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8584)
  covalent geometry    : angle       0.66364 (11724)
  hydrogen bonds       : bond        0.04978 (  487)
  hydrogen bonds       : angle       4.18709 ( 1455)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9121 (mtp) cc_final: 0.8856 (mtm)
REVERT: A   88 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8473 (mm)
REVERT: A  129 MET cc_start: 0.9145 (mtp) cc_final: 0.8690 (mtp)
REVERT: A  286 GLN cc_start: 0.8537 (tt0) cc_final: 0.8236 (tt0)
REVERT: A  295 ARG cc_start: 0.7615 (mtp-110) cc_final: 0.6771 (mmt180)
REVERT: A  313 CYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7726 (m)
REVERT: A  433 LYS cc_start: 0.8743 (tptt) cc_final: 0.8348 (tptp)
REVERT: A  514 MET cc_start: 0.9011 (mtm) cc_final: 0.8731 (mtm)
REVERT: B   69 MET cc_start: 0.9119 (mtp) cc_final: 0.8856 (mtm)
REVERT: B   88 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8494 (mm)
REVERT: B  129 MET cc_start: 0.9146 (mtp) cc_final: 0.8629 (mtp)
REVERT: B  295 ARG cc_start: 0.7654 (mtp-110) cc_final: 0.6806 (mpt180)
REVERT: B  313 CYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7725 (m)
REVERT: B  411 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8200 (tttt)
REVERT: B  433 LYS cc_start: 0.8737 (tptt) cc_final: 0.8302 (tptm)
REVERT: B  446 ASN cc_start: 0.8740 (m-40) cc_final: 0.8529 (m-40)
REVERT: B  514 MET cc_start: 0.9008 (mtm) cc_final: 0.8746 (mtm)
  outliers start: 22
  outliers final: 9
  residues processed: 127
  average time/residue: 0.4802
  time to fit residues: 65.0303
Evaluate side-chains
  122 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  313 CYS
Chi-restraints excluded: chain A residue  411 LYS
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  313 CYS
Chi-restraints excluded: chain B residue  411 LYS
Chi-restraints excluded: chain B residue  519 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0970
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A 286 GLN
B   6 GLN
B 286 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.129779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.106122 restraints weight = 8840.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.33
r_work: 0.2930 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8584  Z= 0.135
  Angle     :  0.639   7.520  11724  Z= 0.309
  Chirality :  0.042   0.154   1394
  Planarity :  0.006   0.054   1414
  Dihedral  : 10.432 152.618   1332
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 10.32 %
    Favored  : 86.73 %
  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:  0.40 (0.27), residues: 1052
  helix:  1.14 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop : -2.08 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 112 
 TYR   0.006   0.001   TYR B 500 
 PHE   0.013   0.001   PHE B 350 
 TRP   0.019   0.002   TRP A 410 
 HIS   0.001   0.000   HIS A 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8584)
  covalent geometry    : angle       0.63908 (11724)
  hydrogen bonds       : bond        0.04584 (  487)
  hydrogen bonds       : angle       3.89260 ( 1455)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9142 (mtp) cc_final: 0.8899 (mtm)
REVERT: A  101 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8223 (tt0)
REVERT: A  129 MET cc_start: 0.9158 (mtp) cc_final: 0.8652 (mtp)
REVERT: A  286 GLN cc_start: 0.8489 (tt0) cc_final: 0.8265 (tt0)
REVERT: A  295 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.6989 (mpt180)
REVERT: A  409 ASP cc_start: 0.8733 (p0) cc_final: 0.8345 (p0)
REVERT: A  411 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8233 (tttt)
REVERT: A  433 LYS cc_start: 0.8744 (tptt) cc_final: 0.8301 (tptm)
REVERT: A  514 MET cc_start: 0.9008 (mtm) cc_final: 0.8769 (mtm)
REVERT: B   69 MET cc_start: 0.9153 (mtp) cc_final: 0.8915 (mtm)
REVERT: B  101 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8263 (tt0)
REVERT: B  129 MET cc_start: 0.9155 (mtp) cc_final: 0.8647 (mtp)
REVERT: B  286 GLN cc_start: 0.8479 (tt0) cc_final: 0.8226 (tt0)
REVERT: B  295 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.6991 (mpt180)
REVERT: B  409 ASP cc_start: 0.8722 (p0) cc_final: 0.8340 (p0)
REVERT: B  411 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8225 (tttt)
REVERT: B  433 LYS cc_start: 0.8812 (tptt) cc_final: 0.8364 (tptm)
REVERT: B  514 MET cc_start: 0.9000 (mtm) cc_final: 0.8764 (mtm)
  outliers start: 26
  outliers final: 16
  residues processed: 124
  average time/residue: 0.5323
  time to fit residues: 70.1134
Evaluate side-chains
  130 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  411 LYS
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  411 LYS
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  519 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
B   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.125664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.101185 restraints weight = 9027.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 1.37
r_work: 0.2927 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8584  Z= 0.128
  Angle     :  0.618   7.493  11724  Z= 0.298
  Chirality :  0.042   0.153   1394
  Planarity :  0.006   0.052   1414
  Dihedral  : 10.399 152.285   1332
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 11.45 %
    Favored  : 84.92 %
  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 (0.28), residues: 1052
  helix:  1.55 (0.20), residues: 760
  sheet:  None (None), residues: 0
  loop : -1.94 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.005   0.001   TYR B 500 
 PHE   0.012   0.001   PHE B 351 
 TRP   0.019   0.001   TRP A 410 
 HIS   0.001   0.000   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8584)
  covalent geometry    : angle       0.61833 (11724)
  hydrogen bonds       : bond        0.04247 (  487)
  hydrogen bonds       : angle       3.76746 ( 1455)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9141 (mtp) cc_final: 0.8889 (mtm)
REVERT: A   88 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8516 (mm)
REVERT: A   94 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8864 (mm)
REVERT: A  101 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8256 (tt0)
REVERT: A  129 MET cc_start: 0.9160 (mtp) cc_final: 0.8691 (mtp)
REVERT: A  286 GLN cc_start: 0.8452 (tt0) cc_final: 0.8252 (tt0)
REVERT: A  295 ARG cc_start: 0.7770 (mtp-110) cc_final: 0.6977 (mpt180)
REVERT: A  352 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8090 (mp)
REVERT: A  409 ASP cc_start: 0.8689 (p0) cc_final: 0.8310 (p0)
REVERT: A  411 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8287 (tttt)
REVERT: A  433 LYS cc_start: 0.8710 (tptt) cc_final: 0.8321 (tptp)
REVERT: B   69 MET cc_start: 0.9124 (mtp) cc_final: 0.8878 (mtm)
REVERT: B   94 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8861 (mm)
REVERT: B  101 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8274 (tt0)
REVERT: B  129 MET cc_start: 0.9151 (mtp) cc_final: 0.8673 (mtp)
REVERT: B  295 ARG cc_start: 0.7808 (mtp-110) cc_final: 0.6999 (mpt180)
REVERT: B  352 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8079 (mp)
REVERT: B  409 ASP cc_start: 0.8671 (p0) cc_final: 0.8285 (p0)
REVERT: B  433 LYS cc_start: 0.8798 (tptt) cc_final: 0.8341 (tptm)
  outliers start: 32
  outliers final: 15
  residues processed: 131
  average time/residue: 0.5319
  time to fit residues: 74.1953
Evaluate side-chains
  131 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  411 LYS
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   76 SER
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  519 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   chunk 101 optimal weight:    6.9990
   chunk 99 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0770
   chunk 84 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 71 optimal weight:    5.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
B   6 GLN
B 286 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.127595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.103405 restraints weight = 8960.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 1.36
r_work: 0.2946 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8584  Z= 0.112
  Angle     :  0.590   7.209  11724  Z= 0.284
  Chirality :  0.041   0.153   1394
  Planarity :  0.005   0.050   1414
  Dihedral  : 10.290 152.034   1332
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 12.47 %
    Favored  : 84.01 %
  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:  1.28 (0.28), residues: 1052
  helix:  1.85 (0.20), residues: 756
  sheet:  None (None), residues: 0
  loop : -1.90 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 108 
 TYR   0.004   0.001   TYR A 429 
 PHE   0.011   0.001   PHE A 351 
 TRP   0.018   0.001   TRP A 410 
 HIS   0.002   0.000   HIS B 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8584)
  covalent geometry    : angle       0.58998 (11724)
  hydrogen bonds       : bond        0.03689 (  487)
  hydrogen bonds       : angle       3.63905 ( 1455)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7506 (mt-10)
REVERT: A   69 MET cc_start: 0.9086 (mtp) cc_final: 0.8850 (mtm)
REVERT: A   88 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8474 (mm)
REVERT: A  101 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8173 (tt0)
REVERT: A  129 MET cc_start: 0.9145 (mtp) cc_final: 0.8649 (mtp)
REVERT: A  286 GLN cc_start: 0.8391 (tt0) cc_final: 0.8127 (tt0)
REVERT: A  295 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.6974 (mpt180)
REVERT: A  352 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8590 (mt)
REVERT: A  409 ASP cc_start: 0.8579 (p0) cc_final: 0.8293 (p0)
REVERT: A  433 LYS cc_start: 0.8716 (tptt) cc_final: 0.8322 (tptp)
REVERT: B   69 MET cc_start: 0.9090 (mtp) cc_final: 0.8857 (mtm)
REVERT: B   88 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8482 (mm)
REVERT: B  101 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8220 (tt0)
REVERT: B  129 MET cc_start: 0.9135 (mtp) cc_final: 0.8632 (mtp)
REVERT: B  286 GLN cc_start: 0.8412 (tt0) cc_final: 0.8160 (tt0)
REVERT: B  295 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.6947 (mpt180)
REVERT: B  352 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8594 (mt)
REVERT: B  433 LYS cc_start: 0.8783 (tptt) cc_final: 0.8312 (tptm)
  outliers start: 31
  outliers final: 12
  residues processed: 130
  average time/residue: 0.4767
  time to fit residues: 65.9348
Evaluate side-chains
  128 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  519 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 78 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0050
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
B   6 GLN
B 256 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.127413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.103022 restraints weight = 8918.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 1.37
r_work: 0.2941 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8584  Z= 0.116
  Angle     :  0.597   7.136  11724  Z= 0.287
  Chirality :  0.041   0.151   1394
  Planarity :  0.005   0.051   1414
  Dihedral  : 10.255 151.739   1332
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 12.81 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.28), residues: 1052
  helix:  2.02 (0.20), residues: 754
  sheet:  None (None), residues: 0
  loop : -1.85 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 120 
 TYR   0.006   0.001   TYR A 500 
 PHE   0.011   0.001   PHE A 351 
 TRP   0.017   0.001   TRP A 410 
 HIS   0.002   0.000   HIS B 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8584)
  covalent geometry    : angle       0.59664 (11724)
  hydrogen bonds       : bond        0.03788 (  487)
  hydrogen bonds       : angle       3.62422 ( 1455)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7563 (mt-10)
REVERT: A   69 MET cc_start: 0.9115 (mtp) cc_final: 0.8845 (mtm)
REVERT: A   88 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8472 (mm)
REVERT: A   94 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8883 (mm)
REVERT: A  101 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8237 (tt0)
REVERT: A  129 MET cc_start: 0.9174 (mtp) cc_final: 0.8705 (mtp)
REVERT: A  295 ARG cc_start: 0.7853 (mtp-110) cc_final: 0.7001 (mpt180)
REVERT: A  352 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8185 (mp)
REVERT: A  433 LYS cc_start: 0.8718 (tptt) cc_final: 0.8339 (tptp)
REVERT: B    6 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6621 (mt0)
REVERT: B   69 MET cc_start: 0.9135 (mtp) cc_final: 0.8896 (mtm)
REVERT: B   88 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8487 (mm)
REVERT: B   94 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8883 (mm)
REVERT: B  101 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8258 (tt0)
REVERT: B  129 MET cc_start: 0.9163 (mtp) cc_final: 0.8687 (mtp)
REVERT: B  286 GLN cc_start: 0.8460 (tt0) cc_final: 0.8194 (tt0)
REVERT: B  295 ARG cc_start: 0.7786 (mtp-110) cc_final: 0.6968 (mpt180)
REVERT: B  352 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8634 (mt)
REVERT: B  433 LYS cc_start: 0.8814 (tptt) cc_final: 0.8359 (tptm)
  outliers start: 30
  outliers final: 15
  residues processed: 129
  average time/residue: 0.4701
  time to fit residues: 64.6805
Evaluate side-chains
  135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  519 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 102 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 104 optimal weight:    0.3980
   chunk 88 optimal weight:    0.0870
   overall best weight:    0.6562

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
B   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.127644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.103372 restraints weight = 8975.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 1.36
r_work: 0.2894 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8584  Z= 0.116
  Angle     :  0.600   7.201  11724  Z= 0.289
  Chirality :  0.041   0.151   1394
  Planarity :  0.005   0.050   1414
  Dihedral  : 10.233 151.863   1332
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 13.83 %
    Favored  : 82.77 %
  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:  1.58 (0.28), residues: 1052
  helix:  2.09 (0.20), residues: 754
  sheet:  None (None), residues: 0
  loop : -1.80 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 108 
 TYR   0.005   0.001   TYR A 500 
 PHE   0.011   0.001   PHE A 351 
 TRP   0.016   0.001   TRP A 410 
 HIS   0.002   0.000   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8584)
  covalent geometry    : angle       0.60037 (11724)
  hydrogen bonds       : bond        0.03727 (  487)
  hydrogen bonds       : angle       3.59811 ( 1455)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 108
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7329 (mt-10)
REVERT: A   69 MET cc_start: 0.9086 (mtp) cc_final: 0.8855 (mtm)
REVERT: A   88 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8424 (mm)
REVERT: A   94 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8857 (mm)
REVERT: A  101 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8258 (tt0)
REVERT: A  129 MET cc_start: 0.9157 (mtp) cc_final: 0.8700 (mtp)
REVERT: A  295 ARG cc_start: 0.7844 (mtp-110) cc_final: 0.6957 (mpt180)
REVERT: A  352 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8186 (mp)
REVERT: A  433 LYS cc_start: 0.8715 (tptt) cc_final: 0.8322 (tptp)
REVERT: B   69 MET cc_start: 0.9105 (mtp) cc_final: 0.8864 (mtm)
REVERT: B   88 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8438 (mm)
REVERT: B   94 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8851 (mm)
REVERT: B  101 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8275 (tt0)
REVERT: B  129 MET cc_start: 0.9151 (mtp) cc_final: 0.8687 (mtp)
REVERT: B  352 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8628 (mt)
REVERT: B  433 LYS cc_start: 0.8795 (tptt) cc_final: 0.8329 (tptm)
  outliers start: 30
  outliers final: 17
  residues processed: 125
  average time/residue: 0.4735
  time to fit residues: 62.9350
Evaluate side-chains
  132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  411 LYS
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  519 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 87 optimal weight:   20.0000
   chunk 29 optimal weight:    4.9990
   chunk 74 optimal weight:    0.3980
   chunk 66 optimal weight:    0.0570
   chunk 14 optimal weight:    0.7980
   chunk 93 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 104 optimal weight:    2.9990
   overall best weight:    0.5900

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
B   6 GLN
B 286 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.128158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.103853 restraints weight = 8965.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 1.37
r_work: 0.2983 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8584  Z= 0.112
  Angle     :  0.591   7.057  11724  Z= 0.284
  Chirality :  0.041   0.150   1394
  Planarity :  0.005   0.050   1414
  Dihedral  : 10.186 151.952   1332
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 13.72 %
    Favored  : 82.54 %
  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:  1.70 (0.28), residues: 1052
  helix:  2.16 (0.20), residues: 754
  sheet:  None (None), residues: 0
  loop : -1.70 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 295 
 TYR   0.005   0.001   TYR B 500 
 PHE   0.011   0.001   PHE B 351 
 TRP   0.016   0.001   TRP A 410 
 HIS   0.002   0.000   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8584)
  covalent geometry    : angle       0.59063 (11724)
  hydrogen bonds       : bond        0.03552 (  487)
  hydrogen bonds       : angle       3.54265 ( 1455)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7320 (mt-10)
REVERT: A   69 MET cc_start: 0.9123 (mtp) cc_final: 0.8861 (mtm)
REVERT: A   88 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8436 (mm)
REVERT: A   94 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8863 (mm)
REVERT: A  101 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8223 (tt0)
REVERT: A  129 MET cc_start: 0.9170 (mtp) cc_final: 0.8711 (mtp)
REVERT: A  295 ARG cc_start: 0.7838 (mtp-110) cc_final: 0.7001 (mpt180)
REVERT: A  352 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8647 (mt)
REVERT: A  433 LYS cc_start: 0.8717 (tptt) cc_final: 0.8330 (tptp)
REVERT: B   69 MET cc_start: 0.9140 (mtp) cc_final: 0.8917 (mtm)
REVERT: B   88 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8451 (mm)
REVERT: B   94 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8862 (mm)
REVERT: B  101 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8203 (tt0)
REVERT: B  129 MET cc_start: 0.9163 (mtp) cc_final: 0.8707 (mtp)
REVERT: B  286 GLN cc_start: 0.8444 (tt0) cc_final: 0.8133 (tt0)
REVERT: B  352 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8642 (mt)
REVERT: B  433 LYS cc_start: 0.8802 (tptt) cc_final: 0.8342 (tptm)
  outliers start: 33
  outliers final: 20
  residues processed: 124
  average time/residue: 0.5537
  time to fit residues: 73.2028
Evaluate side-chains
  132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  304 MET
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  463 LEU
Chi-restraints excluded: chain B residue  519 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A 286 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.125742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.101300 restraints weight = 8912.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 1.36
r_work: 0.2940 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8584  Z= 0.144
  Angle     :  0.638   7.679  11724  Z= 0.308
  Chirality :  0.043   0.153   1394
  Planarity :  0.005   0.051   1414
  Dihedral  : 10.255 151.365   1332
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 14.40 %
    Favored  : 82.20 %
  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:  1.57 (0.28), residues: 1052
  helix:  2.05 (0.20), residues: 752
  sheet:  None (None), residues: 0
  loop : -1.69 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 295 
 TYR   0.008   0.001   TYR B 500 
 PHE   0.013   0.001   PHE B 350 
 TRP   0.016   0.002   TRP A 558 
 HIS   0.001   0.000   HIS B 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8584)
  covalent geometry    : angle       0.63827 (11724)
  hydrogen bonds       : bond        0.04371 (  487)
  hydrogen bonds       : angle       3.64309 ( 1455)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9144 (mtp) cc_final: 0.8892 (mtm)
REVERT: A   88 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8481 (mm)
REVERT: A  101 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8240 (tt0)
REVERT: A  129 MET cc_start: 0.9170 (mtp) cc_final: 0.8701 (mtp)
REVERT: A  295 ARG cc_start: 0.7844 (mtp-110) cc_final: 0.6976 (mpt180)
REVERT: A  352 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8708 (mt)
REVERT: A  409 ASP cc_start: 0.8627 (p0) cc_final: 0.8304 (p0)
REVERT: A  433 LYS cc_start: 0.8704 (tptt) cc_final: 0.8314 (tptp)
REVERT: B   69 MET cc_start: 0.9163 (mtp) cc_final: 0.8906 (mtm)
REVERT: B   88 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8488 (mm)
REVERT: B  101 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8272 (tt0)
REVERT: B  129 MET cc_start: 0.9166 (mtp) cc_final: 0.8696 (mtp)
REVERT: B  286 GLN cc_start: 0.8508 (tt0) cc_final: 0.8235 (tt0)
REVERT: B  352 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8701 (mt)
REVERT: B  409 ASP cc_start: 0.8606 (p0) cc_final: 0.8359 (p0)
REVERT: B  433 LYS cc_start: 0.8797 (tptt) cc_final: 0.8364 (tptm)
  outliers start: 30
  outliers final: 19
  residues processed: 122
  average time/residue: 0.5071
  time to fit residues: 66.0140
Evaluate side-chains
  129 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  304 MET
Chi-restraints excluded: chain B residue  339 LEU
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  519 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 104 optimal weight:    0.4980
   chunk 92 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0370
   chunk 93 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
B   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.127694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.103317 restraints weight = 8921.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 1.37
r_work: 0.2979 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8584  Z= 0.114
  Angle     :  0.599   8.173  11724  Z= 0.288
  Chirality :  0.041   0.151   1394
  Planarity :  0.005   0.050   1414
  Dihedral  : 10.202 152.177   1332
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 14.85 %
    Favored  : 82.31 %
  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:  1.75 (0.28), residues: 1052
  helix:  2.18 (0.20), residues: 752
  sheet:  None (None), residues: 0
  loop : -1.63 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 295 
 TYR   0.005   0.001   TYR B 500 
 PHE   0.011   0.001   PHE A 351 
 TRP   0.016   0.001   TRP A 410 
 HIS   0.002   0.000   HIS B 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 8584)
  covalent geometry    : angle       0.59890 (11724)
  hydrogen bonds       : bond        0.03651 (  487)
  hydrogen bonds       : angle       3.56381 ( 1455)

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

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

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2104 Ramachandran restraints generated.
    1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.9150 (mtp) cc_final: 0.8893 (mtm)
REVERT: A   88 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8444 (mm)
REVERT: A  101 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8221 (tt0)
REVERT: A  129 MET cc_start: 0.9160 (mtp) cc_final: 0.8682 (mtp)
REVERT: A  286 GLN cc_start: 0.8195 (tt0) cc_final: 0.7887 (mt0)
REVERT: A  295 ARG cc_start: 0.7823 (mtp-110) cc_final: 0.6978 (mpt180)
REVERT: A  352 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8668 (mt)
REVERT: B   69 MET cc_start: 0.9144 (mtp) cc_final: 0.8883 (mtm)
REVERT: B   88 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8464 (mm)
REVERT: B  129 MET cc_start: 0.9155 (mtp) cc_final: 0.8681 (mtp)
REVERT: B  286 GLN cc_start: 0.8453 (tt0) cc_final: 0.8216 (tt0)
REVERT: B  352 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8656 (mt)
REVERT: B  433 LYS cc_start: 0.8790 (tptt) cc_final: 0.8349 (tptm)
  outliers start: 25
  outliers final: 16
  residues processed: 125
  average time/residue: 0.4996
  time to fit residues: 66.6480
Evaluate side-chains
  125 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 SER
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  224 CYS
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  463 LEU
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  224 CYS
Chi-restraints excluded: chain B residue  304 MET
Chi-restraints excluded: chain B residue  352 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  519 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 93 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0980
   chunk 96 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A 256 GLN
B   6 GLN
B 256 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.129464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.105386 restraints weight = 8940.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 1.36
r_work: 0.2986 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8584  Z= 0.116
  Angle     :  0.600   8.422  11724  Z= 0.287
  Chirality :  0.041   0.151   1394
  Planarity :  0.005   0.050   1414
  Dihedral  : 10.185 152.143   1332
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 14.29 %
    Favored  : 82.65 %
  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:  1.75 (0.28), residues: 1052
  helix:  2.18 (0.20), residues: 752
  sheet:  None (None), residues: 0
  loop : -1.60 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 295 
 TYR   0.006   0.001   TYR A 500 
 PHE   0.011   0.001   PHE A 351 
 TRP   0.016   0.001   TRP A 410 
 HIS   0.002   0.000   HIS A 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8584)
  covalent geometry    : angle       0.60011 (11724)
  hydrogen bonds       : bond        0.03697 (  487)
  hydrogen bonds       : angle       3.55115 ( 1455)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2645.06 seconds
wall clock time: 45 minutes 37.66 seconds (2737.66 seconds total)