Starting phenix.real_space_refine
on Wed Mar  4 07:06:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b5c_12025/03_2026/7b5c_12025.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b5c_12025/03_2026/7b5c_12025.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b5c_12025/03_2026/7b5c_12025.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b5c_12025/03_2026/7b5c_12025.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b5c_12025/03_2026/7b5c_12025.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b5c_12025/03_2026/7b5c_12025.map"
  }
  resolution = 3.7
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     S      74      5.16       5
     C    7684      2.51       5
     N    1936      2.21       5
     O    2072      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11770
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 718, 5883
          Classifications: {'peptide': 718}
          Link IDs: {'PTRANS': 31, 'TRANS': 686}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.37, per 1000 atoms: 0.46
  Number of scatterers: 11770
  At special positions: 0
  Unit cell: (116.38, 112.332, 114.356, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      4     19.99
     S      74     16.00
     O    2072      8.00
     N    1936      7.00
     C    7684      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 370 " - pdb=" SG  CYS A 395 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 836 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 386 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 625 " - pdb=" SG  CYS A 630 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 370 " - pdb=" SG  CYS B 395 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 836 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 386 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 625 " - pdb=" SG  CYS B 630 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 569.1 milliseconds
  

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2752

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      63.4% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 166 through 181
      Proline residue:  A 177  - end of helix
    Processing helix  chain 'A' and resid 205 through 211
    Processing helix  chain 'A' and resid 242 through 257
    Processing helix  chain 'A' and resid 268 through 275
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 307 through 311
      removed outlier: 3.597A  pdb=" N   PHE A 311 " --> pdb=" O   TYR A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 325
    Processing helix  chain 'A' and resid 325 through 360
      Proline residue:  A 344  - end of helix
    Processing helix  chain 'A' and resid 363 through 368
      removed outlier: 4.247A  pdb=" N   MET A 367 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 393
    Processing helix  chain 'A' and resid 394 through 405
      removed outlier: 4.045A  pdb=" N   ALA A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   LEU A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   PHE A 404 " --> pdb=" O   ALA A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 438
      removed outlier: 4.081A  pdb=" N   VAL A 410 " --> pdb=" O   ASN A 406 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   PHE A 411 " --> pdb=" O   PRO A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 466
    Processing helix  chain 'A' and resid 490 through 519
    Processing helix  chain 'A' and resid 536 through 568
      removed outlier: 3.747A  pdb=" N   ALA A 540 " --> pdb=" O   VAL A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 601
      Proline residue:  A 595  - end of helix
    Processing helix  chain 'A' and resid 617 through 619
      No H-bonds generated for 'chain 'A' and resid 617 through 619'
    Processing helix  chain 'A' and resid 630 through 644
    Processing helix  chain 'A' and resid 648 through 667
      Proline residue:  A 658  - end of helix
    Processing helix  chain 'A' and resid 685 through 690
    Processing helix  chain 'A' and resid 699 through 716
      removed outlier: 4.078A  pdb=" N   PHE A 716 " --> pdb=" O   PHE A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 744
      removed outlier: 3.501A  pdb=" N   PHE A 726 " --> pdb=" O   LEU A 722 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   ARG A 736 " --> pdb=" O   ILE A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 782
      removed outlier: 4.114A  pdb=" N   VAL A 772 " --> pdb=" O   GLY A 768 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ILE A 773 " --> pdb=" O   LYS A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 795
    Processing helix  chain 'A' and resid 803 through 809
    Processing helix  chain 'A' and resid 813 through 817
      removed outlier: 4.115A  pdb=" N   PHE A 817 " --> pdb=" O   VAL A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 886
      removed outlier: 3.922A  pdb=" N   TRP A 858 " --> pdb=" O   SER A 854 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ILE A 886 " --> pdb=" O   VAL A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 909
    Processing helix  chain 'B' and resid 166 through 181
      Proline residue:  B 177  - end of helix
    Processing helix  chain 'B' and resid 205 through 211
    Processing helix  chain 'B' and resid 242 through 257
    Processing helix  chain 'B' and resid 268 through 275
    Processing helix  chain 'B' and resid 296 through 305
    Processing helix  chain 'B' and resid 307 through 311
      removed outlier: 3.597A  pdb=" N   PHE B 311 " --> pdb=" O   TYR B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 325
    Processing helix  chain 'B' and resid 325 through 360
      Proline residue:  B 344  - end of helix
    Processing helix  chain 'B' and resid 363 through 368
      removed outlier: 4.248A  pdb=" N   MET B 367 " --> pdb=" O   ASN B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 393
    Processing helix  chain 'B' and resid 394 through 405
      removed outlier: 4.044A  pdb=" N   ALA B 398 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   LEU B 403 " --> pdb=" O   ARG B 399 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   PHE B 404 " --> pdb=" O   ALA B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 438
      removed outlier: 4.080A  pdb=" N   VAL B 410 " --> pdb=" O   ASN B 406 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   PHE B 411 " --> pdb=" O   PRO B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 466
    Processing helix  chain 'B' and resid 490 through 519
    Processing helix  chain 'B' and resid 536 through 568
      removed outlier: 3.747A  pdb=" N   ALA B 540 " --> pdb=" O   VAL B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 601
      Proline residue:  B 595  - end of helix
    Processing helix  chain 'B' and resid 617 through 619
      No H-bonds generated for 'chain 'B' and resid 617 through 619'
    Processing helix  chain 'B' and resid 630 through 644
    Processing helix  chain 'B' and resid 648 through 667
      Proline residue:  B 658  - end of helix
    Processing helix  chain 'B' and resid 685 through 690
    Processing helix  chain 'B' and resid 699 through 716
      removed outlier: 4.078A  pdb=" N   PHE B 716 " --> pdb=" O   PHE B 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 722 through 744
      removed outlier: 3.501A  pdb=" N   PHE B 726 " --> pdb=" O   LEU B 722 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   ARG B 736 " --> pdb=" O   ILE B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 759 through 782
      removed outlier: 4.113A  pdb=" N   VAL B 772 " --> pdb=" O   GLY B 768 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   ILE B 773 " --> pdb=" O   LYS B 769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 785 through 795
    Processing helix  chain 'B' and resid 803 through 809
    Processing helix  chain 'B' and resid 813 through 817
      removed outlier: 4.116A  pdb=" N   PHE B 817 " --> pdb=" O   VAL B 814 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 854 through 886
      removed outlier: 3.921A  pdb=" N   TRP B 858 " --> pdb=" O   SER B 854 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE B 886 " --> pdb=" O   VAL B 882 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 890 through 909
    Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 218
    Processing sheet with id=AA2, first strand: chain 'A' and resid 615 through 616
      removed outlier: 3.514A  pdb=" N   ILE A 616 " --> pdb=" O   PHE A 620 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE A 620 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 217 through 218
    Processing sheet with id=AA4, first strand: chain 'B' and resid 615 through 616
      removed outlier: 3.514A  pdb=" N   ILE B 616 " --> pdb=" O   PHE B 620 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE B 620 " --> pdb=" O   ILE B 616 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    642 hydrogen bonds defined for protein.
    1902 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: 1.72

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 3642
        1.35 -     1.47: 3075
        1.47 -     1.59: 5225
        1.59 -     1.71: 0
        1.71 -     1.83: 122
  Bond restraints: 12064
  Sorted by residual:
  bond pdb=" C   MET A 378 "
       pdb=" N   CYS A 379 "
    ideal  model  delta    sigma   weight residual
    1.333  1.292  0.041 1.59e-02 3.96e+03 6.55e+00
  bond pdb=" C   MET B 378 "
       pdb=" N   CYS B 379 "
    ideal  model  delta    sigma   weight residual
    1.333  1.292  0.040 1.59e-02 3.96e+03 6.48e+00
  bond pdb=" C   SER A 527 "
       pdb=" N   PRO A 528 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 2.34e-02 1.83e+03 2.50e+00
  bond pdb=" CA  ILE A 343 "
       pdb=" C   ILE A 343 "
    ideal  model  delta    sigma   weight residual
    1.523  1.538 -0.014 9.20e-03 1.18e+04 2.48e+00
  bond pdb=" CA  ILE B 343 "
       pdb=" C   ILE B 343 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 9.20e-03 1.18e+04 2.43e+00
  ... (remaining 12059 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 16014
        2.65 -     5.29: 263
        5.29 -     7.94: 39
        7.94 -    10.59: 2
       10.59 -    13.23: 2
  Bond angle restraints: 16320
  Sorted by residual:
  angle pdb=" N   VAL B 536 "
        pdb=" CA  VAL B 536 "
        pdb=" C   VAL B 536 "
      ideal   model   delta    sigma   weight residual
     113.53  106.75    6.78 9.80e-01 1.04e+00 4.79e+01
  angle pdb=" N   VAL A 536 "
        pdb=" CA  VAL A 536 "
        pdb=" C   VAL A 536 "
      ideal   model   delta    sigma   weight residual
     113.53  106.75    6.78 9.80e-01 1.04e+00 4.79e+01
  angle pdb=" C   THR B 235 "
        pdb=" N   ASP B 236 "
        pdb=" CA  ASP B 236 "
      ideal   model   delta    sigma   weight residual
     121.54  129.35   -7.81 1.91e+00 2.74e-01 1.67e+01
  angle pdb=" C   THR A 235 "
        pdb=" N   ASP A 236 "
        pdb=" CA  ASP A 236 "
      ideal   model   delta    sigma   weight residual
     121.54  129.34   -7.80 1.91e+00 2.74e-01 1.67e+01
  angle pdb=" CA  LEU B 722 "
        pdb=" CB  LEU B 722 "
        pdb=" CG  LEU B 722 "
      ideal   model   delta    sigma   weight residual
     116.30  129.53  -13.23 3.50e+00 8.16e-02 1.43e+01
  ... (remaining 16315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 6340
       17.88 -    35.77: 720
       35.77 -    53.65: 130
       53.65 -    71.54: 18
       71.54 -    89.42: 10
  Dihedral angle restraints: 7218
    sinusoidal: 2966
      harmonic: 4252
  Sorted by residual:
  dihedral pdb=" CB  CYS A 382 "
           pdb=" SG  CYS A 382 "
           pdb=" SG  CYS A 386 "
           pdb=" CB  CYS A 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.69   45.31     1      1.00e+01 1.00e-02 2.85e+01
  dihedral pdb=" CB  CYS B 382 "
           pdb=" SG  CYS B 382 "
           pdb=" SG  CYS B 386 "
           pdb=" CB  CYS B 386 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.70   45.30     1      1.00e+01 1.00e-02 2.85e+01
  dihedral pdb=" CA  CYS A 370 "
           pdb=" C   CYS A 370 "
           pdb=" N   ASP A 371 "
           pdb=" CA  ASP A 371 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.90   25.10     0      5.00e+00 4.00e-02 2.52e+01
  ... (remaining 7215 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1301
       0.051 -    0.103: 388
       0.103 -    0.154: 89
       0.154 -    0.206: 14
       0.206 -    0.257: 4
  Chirality restraints: 1796
  Sorted by residual:
  chirality pdb=" CB  VAL B 310 "
            pdb=" CA  VAL B 310 "
            pdb=" CG1 VAL B 310 "
            pdb=" CG2 VAL B 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CB  VAL A 310 "
            pdb=" CA  VAL A 310 "
            pdb=" CG1 VAL A 310 "
            pdb=" CG2 VAL A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CB  VAL B 569 "
            pdb=" CA  VAL B 569 "
            pdb=" CG1 VAL B 569 "
            pdb=" CG2 VAL B 569 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 1793 not shown)

  Planarity restraints: 2044
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 203 "   -0.055 5.00e-02 4.00e+02   8.18e-02 1.07e+01
        pdb=" N   PRO B 204 "    0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO B 204 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 204 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 203 "    0.054 5.00e-02 4.00e+02   8.17e-02 1.07e+01
        pdb=" N   PRO A 204 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO A 204 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 204 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 723 "    0.051 5.00e-02 4.00e+02   7.65e-02 9.37e+00
        pdb=" N   PRO A 724 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A 724 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 724 "    0.043 5.00e-02 4.00e+02
  ... (remaining 2041 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2381
        2.77 -     3.30: 11383
        3.30 -     3.84: 19670
        3.84 -     4.37: 21569
        4.37 -     4.90: 37092
  Nonbonded interactions: 92095
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 740 "
            pdb=" OG1 THR A 744 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   LYS B 740 "
            pdb=" OG1 THR B 744 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   ALA A 600 "
            pdb=" OG1 THR A 782 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   ALA B 600 "
            pdb=" OG1 THR B 782 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OH  TYR A 791 "
            pdb=" O   HIS A 802 "
     model   vdw
     2.257 3.040
  ... (remaining 92090 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  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:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.520
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12072  Z= 0.231
  Angle     :  0.870  13.232  16336  Z= 0.491
  Chirality :  0.052   0.257   1796
  Planarity :  0.008   0.082   2044
  Dihedral  : 15.211  89.423   4442
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  8.75 %
    Favored  : 90.47 %
  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: -3.64 (0.18), residues: 1416
  helix: -1.58 (0.15), residues: 838
  sheet: -2.47 (0.87), residues: 32
  loop : -3.72 (0.20), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 321 
 TYR   0.018   0.002   TYR A 222 
 PHE   0.019   0.002   PHE B 589 
 TRP   0.028   0.002   TRP B 427 
 HIS   0.007   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 (12064)
  covalent geometry    : angle       0.85675 (16320)
  SS BOND              : bond        0.00914 (    8)
  SS BOND              : angle       4.87638 (   16)
  hydrogen bonds       : bond        0.07470 (  642)
  hydrogen bonds       : angle       5.54449 ( 1902)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 250
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 PHE cc_start: 0.5415 (t80) cc_final: 0.5122 (t80)
REVERT: A  446 GLU cc_start: 0.5564 (OUTLIER) cc_final: 0.5343 (mm-30)
REVERT: A  524 MET cc_start: 0.2652 (ptt) cc_final: 0.1590 (ttt)
REVERT: A  560 ILE cc_start: 0.8464 (tp) cc_final: 0.8245 (tt)
REVERT: B  341 MET cc_start: 0.7809 (mmm) cc_final: 0.7602 (mmm)
REVERT: B  351 ILE cc_start: 0.8798 (tp) cc_final: 0.8465 (pt)
REVERT: B  418 LEU cc_start: 0.8079 (tt) cc_final: 0.7478 (mp)
REVERT: B  446 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5631 (mm-30)
REVERT: B  515 ARG cc_start: 0.6786 (tpm170) cc_final: 0.6103 (ttt180)
REVERT: B  524 MET cc_start: 0.2614 (ptt) cc_final: 0.1569 (ttt)
REVERT: B  666 TYR cc_start: 0.3989 (t80) cc_final: 0.3436 (m-80)
  outliers start: 10
  outliers final: 1
  residues processed: 258
  average time/residue: 0.1460
  time to fit residues: 49.8141
Evaluate side-chains
  164 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 161
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  905 VAL
Chi-restraints excluded: chain B residue  446 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    0.1980
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.1980
   chunk 55 optimal weight:    6.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
A 431 GLN
A 709 GLN
A 731 ASN
B 709 GLN
B 731 ASN
B 895 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.146263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.119151 restraints weight = 18057.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.119640 restraints weight = 13850.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.119832 restraints weight = 11041.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.120556 restraints weight = 10454.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.120699 restraints weight = 9232.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12072  Z= 0.129
  Angle     :  0.624  10.145  16336  Z= 0.324
  Chirality :  0.041   0.150   1796
  Planarity :  0.006   0.077   2044
  Dihedral  :  5.926  69.970   1591
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.84 %
    Favored  : 82.73 %
  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: -2.14 (0.20), residues: 1416
  helix: -0.14 (0.17), residues: 838
  sheet: -2.09 (0.92), residues: 32
  loop : -3.50 (0.22), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 213 
 TYR   0.017   0.001   TYR A 251 
 PHE   0.028   0.001   PHE B 617 
 TRP   0.022   0.001   TRP B 427 
 HIS   0.009   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (12064)
  covalent geometry    : angle       0.61460 (16320)
  SS BOND              : bond        0.00444 (    8)
  SS BOND              : angle       3.58455 (   16)
  hydrogen bonds       : bond        0.04615 (  642)
  hydrogen bonds       : angle       4.86671 ( 1902)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 196
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 PHE cc_start: 0.5157 (t80) cc_final: 0.4940 (t80)
REVERT: A  391 MET cc_start: 0.8093 (tpt) cc_final: 0.7892 (tpt)
REVERT: A  418 LEU cc_start: 0.8079 (tt) cc_final: 0.7655 (mp)
REVERT: A  446 GLU cc_start: 0.5625 (OUTLIER) cc_final: 0.5383 (mm-30)
REVERT: A  491 PHE cc_start: 0.4734 (t80) cc_final: 0.4482 (t80)
REVERT: A  524 MET cc_start: 0.2346 (ptt) cc_final: 0.1428 (ttt)
REVERT: A  560 ILE cc_start: 0.8559 (tp) cc_final: 0.8254 (tt)
REVERT: A  617 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5508 (m-80)
REVERT: A  904 MET cc_start: 0.6339 (mtp) cc_final: 0.5746 (mtp)
REVERT: B  215 GLN cc_start: 0.7458 (tp40) cc_final: 0.7244 (tm-30)
REVERT: B  381 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6636 (pp)
REVERT: B  418 LEU cc_start: 0.7949 (tt) cc_final: 0.7492 (mp)
REVERT: B  446 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.5583 (mm-30)
REVERT: B  515 ARG cc_start: 0.6670 (tpm170) cc_final: 0.5994 (ttt180)
REVERT: B  524 MET cc_start: 0.2217 (ptt) cc_final: 0.1345 (ttt)
REVERT: B  560 ILE cc_start: 0.8618 (tp) cc_final: 0.8283 (tt)
REVERT: B  666 TYR cc_start: 0.3973 (t80) cc_final: 0.3322 (m-80)
REVERT: B  731 ASN cc_start: 0.8554 (m-40) cc_final: 0.8255 (m-40)
  outliers start: 31
  outliers final: 9
  residues processed: 217
  average time/residue: 0.1204
  time to fit residues: 36.5251
Evaluate side-chains
  180 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 167
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  431 GLN
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  617 PHE
Chi-restraints excluded: chain A residue  849 HIS
Chi-restraints excluded: chain A residue  883 ASP
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  446 GLU
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  849 HIS
Chi-restraints excluded: chain B residue  883 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 130 optimal weight:    3.9990
   chunk 15 optimal weight:    0.4980
   chunk 93 optimal weight:    0.9980
   chunk 102 optimal weight:   10.0000
   chunk 105 optimal weight:    9.9990
   chunk 7 optimal weight:    0.1980
   chunk 60 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0570
   chunk 95 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.4698

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.147078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.119608 restraints weight = 18308.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.120084 restraints weight = 13876.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.120324 restraints weight = 11290.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.120988 restraints weight = 10527.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.121095 restraints weight = 9368.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12072  Z= 0.123
  Angle     :  0.618  10.477  16336  Z= 0.313
  Chirality :  0.040   0.145   1796
  Planarity :  0.005   0.076   2044
  Dihedral  :  5.718  70.270   1590
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.88 %
    Favored  : 80.86 %
  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: -1.39 (0.21), residues: 1416
  helix:  0.48 (0.17), residues: 848
  sheet: -2.01 (0.88), residues: 32
  loop : -3.28 (0.23), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 748 
 TYR   0.022   0.001   TYR B 182 
 PHE   0.019   0.001   PHE A 696 
 TRP   0.021   0.001   TRP A 427 
 HIS   0.007   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (12064)
  covalent geometry    : angle       0.60740 (16320)
  SS BOND              : bond        0.00256 (    8)
  SS BOND              : angle       3.72491 (   16)
  hydrogen bonds       : bond        0.04372 (  642)
  hydrogen bonds       : angle       4.74571 ( 1902)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 187
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 MET cc_start: 0.7885 (tpp) cc_final: 0.7596 (ttt)
REVERT: A  418 LEU cc_start: 0.7998 (tt) cc_final: 0.7687 (mp)
REVERT: A  446 GLU cc_start: 0.5729 (OUTLIER) cc_final: 0.5454 (mm-30)
REVERT: A  491 PHE cc_start: 0.4843 (t80) cc_final: 0.4600 (t80)
REVERT: A  524 MET cc_start: 0.2204 (ptt) cc_final: 0.1509 (ttt)
REVERT: A  560 ILE cc_start: 0.8571 (tp) cc_final: 0.8248 (tt)
REVERT: B  381 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6659 (pp)
REVERT: B  418 LEU cc_start: 0.7862 (tt) cc_final: 0.7552 (mp)
REVERT: B  446 GLU cc_start: 0.5775 (OUTLIER) cc_final: 0.5429 (mm-30)
REVERT: B  515 ARG cc_start: 0.6714 (tpm170) cc_final: 0.6096 (ttt180)
REVERT: B  524 MET cc_start: 0.1968 (ptt) cc_final: 0.1179 (ttt)
REVERT: B  560 ILE cc_start: 0.8593 (tp) cc_final: 0.8225 (tt)
REVERT: B  666 TYR cc_start: 0.3973 (t80) cc_final: 0.3290 (m-80)
REVERT: B  731 ASN cc_start: 0.8456 (m-40) cc_final: 0.8227 (m-40)
  outliers start: 29
  outliers final: 13
  residues processed: 210
  average time/residue: 0.1188
  time to fit residues: 35.5762
Evaluate side-chains
  184 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 168
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 ARG
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  849 HIS
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  411 PHE
Chi-restraints excluded: chain B residue  446 GLU
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  849 HIS
Chi-restraints excluded: chain B residue  883 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 107 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   chunk 88 optimal weight:    4.9990
   chunk 92 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 46 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0170
   chunk 45 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    2.5624

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN
A 431 GLN
B 215 GLN
B 431 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.141360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.113941 restraints weight = 18533.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.114154 restraints weight = 13842.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.114481 restraints weight = 11962.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.114780 restraints weight = 10909.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.115256 restraints weight = 10160.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12072  Z= 0.205
  Angle     :  0.690   9.856  16336  Z= 0.355
  Chirality :  0.044   0.156   1796
  Planarity :  0.006   0.073   2044
  Dihedral  :  5.833  71.201   1590
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.81 %
    Favored  : 79.30 %
  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: -1.36 (0.22), residues: 1416
  helix:  0.48 (0.17), residues: 848
  sheet: -1.58 (0.95), residues: 32
  loop : -3.25 (0.23), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 125 
 TYR   0.017   0.002   TYR B 182 
 PHE   0.020   0.002   PHE A 696 
 TRP   0.015   0.002   TRP B 760 
 HIS   0.008   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 (12064)
  covalent geometry    : angle       0.67205 (16320)
  SS BOND              : bond        0.00667 (    8)
  SS BOND              : angle       4.99080 (   16)
  hydrogen bonds       : bond        0.04863 (  642)
  hydrogen bonds       : angle       4.80469 ( 1902)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 183
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 LEU cc_start: 0.8288 (tt) cc_final: 0.7759 (mp)
REVERT: A  446 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5577 (tm-30)
REVERT: A  491 PHE cc_start: 0.5131 (t80) cc_final: 0.4915 (t80)
REVERT: A  515 ARG cc_start: 0.6786 (tpm170) cc_final: 0.5981 (ttt180)
REVERT: A  524 MET cc_start: 0.2367 (ptt) cc_final: 0.1594 (ttt)
REVERT: A  560 ILE cc_start: 0.8597 (tp) cc_final: 0.8261 (tt)
REVERT: A  622 MET cc_start: 0.3249 (mmm) cc_final: 0.2929 (mmm)
REVERT: B  381 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6589 (pp)
REVERT: B  418 LEU cc_start: 0.8227 (tt) cc_final: 0.7612 (mp)
REVERT: B  515 ARG cc_start: 0.6763 (tpm170) cc_final: 0.6077 (ttt180)
REVERT: B  524 MET cc_start: 0.2393 (ptt) cc_final: 0.1401 (ttt)
REVERT: B  560 ILE cc_start: 0.8603 (tp) cc_final: 0.8242 (tt)
REVERT: B  666 TYR cc_start: 0.3944 (t80) cc_final: 0.3268 (m-80)
REVERT: B  731 ASN cc_start: 0.8735 (m-40) cc_final: 0.8427 (m-40)
  outliers start: 37
  outliers final: 20
  residues processed: 209
  average time/residue: 0.1098
  time to fit residues: 32.6465
Evaluate side-chains
  192 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  230 HIS
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  849 HIS
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  849 HIS
Chi-restraints excluded: chain B residue  878 MET
Chi-restraints excluded: chain B residue  883 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 116 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 136 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 127 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0670
   chunk 132 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   overall best weight:    1.9724

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN
A 431 GLN
B 215 GLN
B 431 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.142084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.114578 restraints weight = 18413.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.114667 restraints weight = 13585.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.114892 restraints weight = 11629.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.115332 restraints weight = 11002.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.115437 restraints weight = 10134.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12072  Z= 0.173
  Angle     :  0.653  10.056  16336  Z= 0.336
  Chirality :  0.043   0.152   1796
  Planarity :  0.005   0.073   2044
  Dihedral  :  5.417  72.431   1587
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 18.52 %
    Favored  : 77.89 %
  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: -1.13 (0.22), residues: 1416
  helix:  0.65 (0.18), residues: 844
  sheet: -1.35 (0.98), residues: 32
  loop : -3.11 (0.23), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 748 
 TYR   0.027   0.002   TYR B 251 
 PHE   0.019   0.001   PHE B 617 
 TRP   0.020   0.001   TRP B 427 
 HIS   0.008   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (12064)
  covalent geometry    : angle       0.63848 (16320)
  SS BOND              : bond        0.00602 (    8)
  SS BOND              : angle       4.49405 (   16)
  hydrogen bonds       : bond        0.04767 (  642)
  hydrogen bonds       : angle       4.76041 ( 1902)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 167
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
REVERT: A  446 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.5482 (tm-30)
REVERT: A  491 PHE cc_start: 0.5084 (t80) cc_final: 0.4864 (t80)
REVERT: A  515 ARG cc_start: 0.6815 (tpm170) cc_final: 0.6074 (ttt180)
REVERT: A  524 MET cc_start: 0.2227 (ptt) cc_final: 0.1483 (ttt)
REVERT: A  560 ILE cc_start: 0.8584 (tp) cc_final: 0.8246 (tt)
REVERT: B  381 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6574 (pp)
REVERT: B  418 LEU cc_start: 0.8170 (tt) cc_final: 0.7638 (mp)
REVERT: B  515 ARG cc_start: 0.6727 (tpm170) cc_final: 0.6086 (ttt180)
REVERT: B  524 MET cc_start: 0.2610 (ptt) cc_final: 0.1545 (ttt)
REVERT: B  560 ILE cc_start: 0.8577 (tp) cc_final: 0.8224 (tt)
REVERT: B  731 ASN cc_start: 0.8639 (m-40) cc_final: 0.8363 (m-40)
  outliers start: 46
  outliers final: 26
  residues processed: 199
  average time/residue: 0.1191
  time to fit residues: 33.6252
Evaluate side-chains
  189 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 ARG
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  230 HIS
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  849 HIS
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  431 GLN
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  794 MET
Chi-restraints excluded: chain B residue  829 LEU
Chi-restraints excluded: chain B residue  849 HIS
Chi-restraints excluded: chain B residue  883 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 126 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 133 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 124 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 71 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B 215 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.143697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.116335 restraints weight = 18508.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.115783 restraints weight = 14593.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.116282 restraints weight = 13031.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.116490 restraints weight = 12043.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.117909 restraints weight = 10783.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12072  Z= 0.151
  Angle     :  0.655  10.059  16336  Z= 0.334
  Chirality :  0.041   0.153   1796
  Planarity :  0.005   0.074   2044
  Dihedral  :  5.433  73.358   1587
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.94 %
    Favored  : 76.33 %
  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: -0.91 (0.22), residues: 1416
  helix:  0.82 (0.18), residues: 836
  sheet: -1.19 (1.00), residues: 32
  loop : -2.96 (0.24), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 213 
 TYR   0.019   0.001   TYR B 251 
 PHE   0.016   0.001   PHE A 617 
 TRP   0.023   0.001   TRP B 427 
 HIS   0.007   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12064)
  covalent geometry    : angle       0.63474 (16320)
  SS BOND              : bond        0.00777 (    8)
  SS BOND              : angle       5.19070 (   16)
  hydrogen bonds       : bond        0.04628 (  642)
  hydrogen bonds       : angle       4.70924 ( 1902)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 178
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 LEU cc_start: 0.8120 (tt) cc_final: 0.7697 (mp)
REVERT: A  431 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7952 (tt0)
REVERT: A  491 PHE cc_start: 0.5136 (t80) cc_final: 0.4895 (t80)
REVERT: A  515 ARG cc_start: 0.6704 (tpm170) cc_final: 0.6007 (ttt180)
REVERT: A  524 MET cc_start: 0.2226 (ptt) cc_final: 0.1559 (ttt)
REVERT: A  560 ILE cc_start: 0.8574 (tp) cc_final: 0.8234 (tt)
REVERT: B  418 LEU cc_start: 0.8060 (tt) cc_final: 0.7595 (mp)
REVERT: B  515 ARG cc_start: 0.6713 (tpm170) cc_final: 0.6010 (ttt180)
REVERT: B  524 MET cc_start: 0.2463 (ptt) cc_final: 0.1499 (ttt)
REVERT: B  560 ILE cc_start: 0.8587 (tp) cc_final: 0.8241 (tt)
REVERT: B  731 ASN cc_start: 0.8606 (m-40) cc_final: 0.8356 (m-40)
  outliers start: 35
  outliers final: 25
  residues processed: 203
  average time/residue: 0.1211
  time to fit residues: 34.5666
Evaluate side-chains
  185 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 159
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 ARG
Chi-restraints excluded: chain A residue  183 HIS
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  230 HIS
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain A residue  431 GLN
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  849 HIS
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  245 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  794 MET
Chi-restraints excluded: chain B residue  829 LEU
Chi-restraints excluded: chain B residue  849 HIS
Chi-restraints excluded: chain B residue  883 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 120 optimal weight:    0.0970
   chunk 54 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 105 optimal weight:   20.0000
   chunk 130 optimal weight:    0.7980
   chunk 110 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 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 215 GLN
B 215 GLN
B 431 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.146632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.119465 restraints weight = 18395.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.119395 restraints weight = 14109.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.120078 restraints weight = 13571.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.120581 restraints weight = 10813.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.120909 restraints weight = 9580.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12072  Z= 0.129
  Angle     :  0.626  10.014  16336  Z= 0.319
  Chirality :  0.041   0.149   1796
  Planarity :  0.005   0.074   2044
  Dihedral  :  4.794  25.491   1584
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 21.09 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.58 (0.22), residues: 1416
  helix:  1.03 (0.18), residues: 842
  sheet: -0.77 (1.04), residues: 32
  loop : -2.78 (0.24), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 213 
 TYR   0.031   0.001   TYR B 251 
 PHE   0.019   0.001   PHE B 617 
 TRP   0.024   0.001   TRP A 427 
 HIS   0.006   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (12064)
  covalent geometry    : angle       0.61274 (16320)
  SS BOND              : bond        0.00626 (    8)
  SS BOND              : angle       4.10004 (   16)
  hydrogen bonds       : bond        0.04368 (  642)
  hydrogen bonds       : angle       4.62640 ( 1902)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 171
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 LEU cc_start: 0.7990 (tt) cc_final: 0.7634 (mp)
REVERT: A  491 PHE cc_start: 0.5109 (t80) cc_final: 0.4861 (t80)
REVERT: A  515 ARG cc_start: 0.6676 (tpm170) cc_final: 0.5977 (ttt180)
REVERT: A  524 MET cc_start: 0.2321 (ptt) cc_final: 0.1768 (ttt)
REVERT: A  560 ILE cc_start: 0.8553 (tp) cc_final: 0.8212 (tt)
REVERT: B  418 LEU cc_start: 0.7980 (tt) cc_final: 0.7586 (mp)
REVERT: B  515 ARG cc_start: 0.6720 (tpm170) cc_final: 0.6066 (ttt180)
REVERT: B  524 MET cc_start: 0.2266 (ptt) cc_final: 0.1517 (ttt)
REVERT: B  560 ILE cc_start: 0.8594 (tp) cc_final: 0.8200 (tt)
REVERT: B  706 MET cc_start: 0.8688 (mmp) cc_final: 0.8317 (mmt)
REVERT: B  731 ASN cc_start: 0.8529 (m-40) cc_final: 0.8235 (m-40)
  outliers start: 35
  outliers final: 26
  residues processed: 199
  average time/residue: 0.1116
  time to fit residues: 31.6362
Evaluate side-chains
  182 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 156
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 ARG
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  849 HIS
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  245 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  431 GLN
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  509 LEU
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  783 SER
Chi-restraints excluded: chain B residue  829 LEU
Chi-restraints excluded: chain B residue  849 HIS
Chi-restraints excluded: chain B residue  883 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   chunk 68 optimal weight:    4.9990
   chunk 124 optimal weight:    2.9990
   chunk 126 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 99 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.145401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.118690 restraints weight = 18399.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.118097 restraints weight = 14882.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.118907 restraints weight = 12221.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.119193 restraints weight = 10856.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.119723 restraints weight = 10092.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12072  Z= 0.145
  Angle     :  0.657  14.175  16336  Z= 0.329
  Chirality :  0.041   0.150   1796
  Planarity :  0.005   0.074   2044
  Dihedral  :  4.747  24.080   1584
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 21.64 %
    Favored  : 75.94 %
  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: -0.54 (0.22), residues: 1416
  helix:  1.04 (0.18), residues: 844
  sheet: -0.69 (1.05), residues: 32
  loop : -2.72 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 213 
 TYR   0.031   0.002   TYR A 251 
 PHE   0.016   0.001   PHE A 617 
 TRP   0.020   0.001   TRP A 427 
 HIS   0.006   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (12064)
  covalent geometry    : angle       0.64592 (16320)
  SS BOND              : bond        0.00509 (    8)
  SS BOND              : angle       3.84707 (   16)
  hydrogen bonds       : bond        0.04467 (  642)
  hydrogen bonds       : angle       4.63996 ( 1902)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 158
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 LEU cc_start: 0.8027 (tt) cc_final: 0.7664 (mp)
REVERT: A  491 PHE cc_start: 0.4999 (t80) cc_final: 0.4792 (t80)
REVERT: A  515 ARG cc_start: 0.6667 (tpm170) cc_final: 0.6013 (ttt180)
REVERT: A  524 MET cc_start: 0.2342 (ptt) cc_final: 0.1803 (ttt)
REVERT: A  560 ILE cc_start: 0.8582 (tp) cc_final: 0.8214 (tt)
REVERT: B  418 LEU cc_start: 0.8024 (tt) cc_final: 0.7616 (mp)
REVERT: B  515 ARG cc_start: 0.6715 (tpm170) cc_final: 0.6061 (ttt180)
REVERT: B  524 MET cc_start: 0.2270 (ptt) cc_final: 0.1466 (ttt)
REVERT: B  560 ILE cc_start: 0.8570 (tp) cc_final: 0.8189 (tt)
REVERT: B  706 MET cc_start: 0.8700 (mmp) cc_final: 0.8336 (mmt)
REVERT: B  731 ASN cc_start: 0.8589 (m-40) cc_final: 0.8283 (m-40)
  outliers start: 31
  outliers final: 24
  residues processed: 181
  average time/residue: 0.1195
  time to fit residues: 30.5041
Evaluate side-chains
  177 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 ARG
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  230 HIS
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  849 HIS
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  245 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  783 SER
Chi-restraints excluded: chain B residue  829 LEU
Chi-restraints excluded: chain B residue  849 HIS
Chi-restraints excluded: chain B residue  883 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 136 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 140 optimal weight:    0.0770
   chunk 98 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.9544

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN
B 431 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.146644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.119547 restraints weight = 18140.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.119514 restraints weight = 14114.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.120126 restraints weight = 12029.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.120466 restraints weight = 10690.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.120847 restraints weight = 9886.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12072  Z= 0.134
  Angle     :  0.647  13.945  16336  Z= 0.324
  Chirality :  0.041   0.148   1796
  Planarity :  0.005   0.074   2044
  Dihedral  :  4.701  22.963   1584
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.64 %
    Favored  : 75.86 %
  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: -0.43 (0.22), residues: 1416
  helix:  1.13 (0.18), residues: 844
  sheet: -0.68 (1.05), residues: 32
  loop : -2.68 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 213 
 TYR   0.028   0.001   TYR A 251 
 PHE   0.016   0.001   PHE B 617 
 TRP   0.022   0.001   TRP A 427 
 HIS   0.006   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (12064)
  covalent geometry    : angle       0.63674 (16320)
  SS BOND              : bond        0.00499 (    8)
  SS BOND              : angle       3.66877 (   16)
  hydrogen bonds       : bond        0.04387 (  642)
  hydrogen bonds       : angle       4.61082 ( 1902)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 159
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 LEU cc_start: 0.7965 (tt) cc_final: 0.7619 (mp)
REVERT: A  491 PHE cc_start: 0.5083 (t80) cc_final: 0.4808 (t80)
REVERT: A  515 ARG cc_start: 0.6686 (tpm170) cc_final: 0.6037 (ttt180)
REVERT: A  524 MET cc_start: 0.2345 (ptt) cc_final: 0.1794 (ttt)
REVERT: A  560 ILE cc_start: 0.8582 (tp) cc_final: 0.8209 (tt)
REVERT: B  418 LEU cc_start: 0.7971 (tt) cc_final: 0.7592 (mp)
REVERT: B  515 ARG cc_start: 0.6773 (tpm170) cc_final: 0.6128 (ttt180)
REVERT: B  524 MET cc_start: 0.2198 (ptt) cc_final: 0.1471 (ttt)
REVERT: B  560 ILE cc_start: 0.8565 (tp) cc_final: 0.8185 (tt)
REVERT: B  706 MET cc_start: 0.8715 (mmp) cc_final: 0.8327 (mmt)
REVERT: B  731 ASN cc_start: 0.8561 (m-40) cc_final: 0.8268 (m-40)
  outliers start: 32
  outliers final: 26
  residues processed: 183
  average time/residue: 0.1130
  time to fit residues: 29.5819
Evaluate side-chains
  181 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 ARG
Chi-restraints excluded: chain A residue  230 HIS
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  849 HIS
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  245 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  431 GLN
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  783 SER
Chi-restraints excluded: chain B residue  829 LEU
Chi-restraints excluded: chain B residue  849 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 131 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0870
   chunk 19 optimal weight:    0.7980
   chunk 128 optimal weight:    0.6980
   chunk 35 optimal weight:   10.0000
   chunk 61 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 72 optimal weight:   10.0000
   overall best weight:    1.0960

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

Flipped N/Q/H residues before XYZ refinement:
B 431 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.146232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.119172 restraints weight = 18359.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.119124 restraints weight = 14086.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.120070 restraints weight = 12019.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.120359 restraints weight = 10984.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.120441 restraints weight = 9581.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12072  Z= 0.139
  Angle     :  0.651  13.844  16336  Z= 0.328
  Chirality :  0.041   0.149   1796
  Planarity :  0.006   0.119   2044
  Dihedral  :  4.676  22.154   1584
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 21.95 %
    Favored  : 75.70 %
  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: -0.38 (0.23), residues: 1416
  helix:  1.11 (0.18), residues: 852
  sheet: -0.73 (1.04), residues: 32
  loop : -2.60 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 213 
 TYR   0.029   0.002   TYR B 277 
 PHE   0.018   0.001   PHE B 617 
 TRP   0.021   0.001   TRP A 427 
 HIS   0.006   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (12064)
  covalent geometry    : angle       0.64107 (16320)
  SS BOND              : bond        0.00480 (    8)
  SS BOND              : angle       3.62230 (   16)
  hydrogen bonds       : bond        0.04400 (  642)
  hydrogen bonds       : angle       4.61667 ( 1902)

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

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

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2832 Ramachandran restraints generated.
    1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 159
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7595 (t80)
REVERT: A  418 LEU cc_start: 0.7948 (tt) cc_final: 0.7545 (mp)
REVERT: A  491 PHE cc_start: 0.5230 (t80) cc_final: 0.4950 (t80)
REVERT: A  515 ARG cc_start: 0.6703 (tpm170) cc_final: 0.6079 (ttt180)
REVERT: A  524 MET cc_start: 0.2526 (ptt) cc_final: 0.1959 (ttt)
REVERT: A  560 ILE cc_start: 0.8581 (tp) cc_final: 0.8198 (tt)
REVERT: B  418 LEU cc_start: 0.7980 (tt) cc_final: 0.7610 (mp)
REVERT: B  515 ARG cc_start: 0.6848 (tpm170) cc_final: 0.6182 (ttt180)
REVERT: B  524 MET cc_start: 0.2128 (ptt) cc_final: 0.1404 (ttt)
REVERT: B  560 ILE cc_start: 0.8570 (tp) cc_final: 0.8186 (tt)
REVERT: B  706 MET cc_start: 0.8705 (mmp) cc_final: 0.8342 (mmt)
REVERT: B  731 ASN cc_start: 0.8584 (m-40) cc_final: 0.8289 (m-40)
  outliers start: 30
  outliers final: 24
  residues processed: 181
  average time/residue: 0.1094
  time to fit residues: 28.5804
Evaluate side-chains
  181 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 156
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 HIS
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  425 GLU
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  849 HIS
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  245 THR
Chi-restraints excluded: chain B residue  367 MET
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  431 GLN
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  783 SER
Chi-restraints excluded: chain B residue  829 LEU
Chi-restraints excluded: chain B residue  849 HIS
Chi-restraints excluded: chain B residue  883 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 117 optimal weight:    5.9990
   chunk 139 optimal weight:    0.8980
   chunk 114 optimal weight:    0.7980
   chunk 102 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.145842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.118608 restraints weight = 18425.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.118482 restraints weight = 14267.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.119436 restraints weight = 13096.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.119846 restraints weight = 10463.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.119895 restraints weight = 9473.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12072  Z= 0.147
  Angle     :  0.662  13.643  16336  Z= 0.333
  Chirality :  0.041   0.150   1796
  Planarity :  0.005   0.074   2044
  Dihedral  :  4.714  25.061   1584
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 22.03 %
    Favored  : 75.94 %
  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: -0.38 (0.23), residues: 1416
  helix:  1.10 (0.18), residues: 852
  sheet: -0.70 (1.04), residues: 32
  loop : -2.59 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 213 
 TYR   0.026   0.002   TYR A 251 
 PHE   0.035   0.001   PHE A 617 
 TRP   0.019   0.001   TRP A 427 
 HIS   0.006   0.001   HIS B 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12064)
  covalent geometry    : angle       0.65236 (16320)
  SS BOND              : bond        0.00505 (    8)
  SS BOND              : angle       3.62338 (   16)
  hydrogen bonds       : bond        0.04464 (  642)
  hydrogen bonds       : angle       4.62174 ( 1902)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1760.44 seconds
wall clock time: 31 minutes 23.86 seconds (1883.86 seconds total)