Starting phenix.real_space_refine
on Tue Jul 29 22:06:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b5c_12025/07_2025/7b5c_12025.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b5c_12025/07_2025/7b5c_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b5c_12025/07_2025/7b5c_12025.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b5c_12025/07_2025/7b5c_12025.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b5c_12025/07_2025/7b5c_12025.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b5c_12025/07_2025/7b5c_12025.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.54, per 1000 atoms: 0.98
  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: 2.53
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 1.04
  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: 2.98

  Time building geometry restraints manager: 3.04 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: 0.05
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:             1.060
  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:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     31.280
  Find NCS groups from input model:        0.190
  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:             0.010
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.780
-------------------------------------------------------------------------------
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 : 7.43
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.64 (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
 TRP   0.028   0.002   TRP B 427 
 HIS   0.007   0.001   HIS A 402 
 PHE   0.019   0.002   PHE B 589 
 TYR   0.018   0.002   TYR A 222 
 ARG   0.011   0.000   ARG B 321 

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

*********************** 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  : 1.223 
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: 0.2653 (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: 0.7479 (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: 0.3073
  time to fit residues: 104.6007
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  : 1.226 
-------------------------------------------------------------------------------
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 119 optimal weight:    7.9990
   chunk 107 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 72 optimal weight:   20.0000
   chunk 57 optimal weight:    3.9990
   chunk 111 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   chunk 128 optimal weight:    1.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN
A 340 GLN
A 431 GLN
A 546 ASN
A 709 GLN
A 731 ASN
B 215 GLN
B 431 GLN
B 709 GLN
B 731 ASN
B 895 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.140232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.112686 restraints weight = 18373.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.112906 restraints weight = 14164.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.113240 restraints weight = 11695.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  12072  Z= 0.221
  Angle     :  0.709  10.203  16336  Z= 0.372
  Chirality :  0.045   0.160   1796
  Planarity :  0.006   0.076   2044
  Dihedral  :  6.147  70.108   1591
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.23 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.20), residues: 1416
  helix: -0.39 (0.16), residues: 846
  sheet: -2.13 (0.91), residues: 32
  loop : -3.65 (0.22), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 427 
 HIS   0.009   0.001   HIS B 402 
 PHE   0.026   0.002   PHE B 617 
 TYR   0.017   0.002   TYR A 182 
 ARG   0.007   0.001   ARG A 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05175 (  642)
  hydrogen bonds       : angle       4.98222 ( 1902)
  SS BOND              : bond        0.00633 (    8)
  SS BOND              : angle       4.09191 (   16)
  covalent geometry    : bond        0.00502 (12064)
  covalent geometry    : angle       0.69721 (16320)

*********************** 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
  229 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 184
  time to evaluate  : 1.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  381 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6858 (pp)
REVERT: A  391 MET cc_start: 0.8220 (tpt) cc_final: 0.8016 (tpt)
REVERT: A  425 GLU cc_start: 0.7069 (tp30) cc_final: 0.6750 (tp30)
REVERT: A  446 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.5472 (mm-30)
REVERT: A  524 MET cc_start: 0.2498 (ptt) cc_final: 0.1381 (ttt)
REVERT: A  560 ILE cc_start: 0.8599 (tp) cc_final: 0.8282 (tt)
REVERT: A  617 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.6032 (m-80)
REVERT: A  731 ASN cc_start: 0.8679 (m-40) cc_final: 0.8413 (m-40)
REVERT: A  904 MET cc_start: 0.6487 (mtp) cc_final: 0.5800 (mtp)
REVERT: B  381 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.6978 (pp)
REVERT: B  446 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5574 (mm-30)
REVERT: B  515 ARG cc_start: 0.6872 (tpm170) cc_final: 0.6159 (ttt180)
REVERT: B  524 MET cc_start: 0.2714 (ptt) cc_final: 0.1573 (ttt)
REVERT: B  560 ILE cc_start: 0.8628 (tp) cc_final: 0.8329 (tt)
REVERT: B  666 TYR cc_start: 0.4087 (t80) cc_final: 0.3376 (m-80)
REVERT: B  731 ASN cc_start: 0.8709 (m-40) cc_final: 0.8415 (m-40)
  outliers start: 45
  outliers final: 18
  residues processed: 215
  average time/residue: 0.2453
  time to fit residues: 74.4089
Evaluate side-chains
  180 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
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  230 HIS
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  381 LEU
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  563 TRP
Chi-restraints excluded: chain A residue  617 PHE
Chi-restraints excluded: chain A residue  709 GLN
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  446 GLU
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  709 GLN
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 1 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0770
   chunk 17 optimal weight:    4.9990
   chunk 78 optimal weight:    0.5980
   chunk 13 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 94 optimal weight:    0.0980
   chunk 40 optimal weight:    5.9990
   chunk 106 optimal weight:    0.0050
   chunk 135 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.3352

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN
A 709 GLN
B 215 GLN
B 709 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.145776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.117669 restraints weight = 18416.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.118226 restraints weight = 14517.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.118571 restraints weight = 11255.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12072  Z= 0.127
  Angle     :  0.638  10.025  16336  Z= 0.326
  Chirality :  0.041   0.147   1796
  Planarity :  0.006   0.077   2044
  Dihedral  :  5.870  71.265   1590
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.44 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.21), residues: 1416
  helix:  0.40 (0.17), residues: 838
  sheet: -1.98 (0.93), residues: 32
  loop : -3.31 (0.22), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 427 
 HIS   0.007   0.001   HIS B 402 
 PHE   0.019   0.001   PHE A 696 
 TYR   0.026   0.002   TYR B 251 
 ARG   0.006   0.000   ARG A 748 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04566 (  642)
  hydrogen bonds       : angle       4.76339 ( 1902)
  SS BOND              : bond        0.00673 (    8)
  SS BOND              : angle       4.22680 (   16)
  covalent geometry    : bond        0.00266 (12064)
  covalent geometry    : angle       0.62476 (16320)

*********************** 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
  211 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 185
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 LEU cc_start: 0.8074 (tt) cc_final: 0.7619 (mp)
REVERT: A  446 GLU cc_start: 0.5732 (OUTLIER) cc_final: 0.5461 (mm-30)
REVERT: A  491 PHE cc_start: 0.5012 (t80) cc_final: 0.4765 (t80)
REVERT: A  524 MET cc_start: 0.2385 (ptt) cc_final: 0.1346 (ttt)
REVERT: A  560 ILE cc_start: 0.8585 (tp) cc_final: 0.8265 (tt)
REVERT: A  617 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.5943 (m-80)
REVERT: A  731 ASN cc_start: 0.8531 (m-40) cc_final: 0.8299 (m-40)
REVERT: B  418 LEU cc_start: 0.7996 (tt) cc_final: 0.7546 (mp)
REVERT: B  446 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5482 (mm-30)
REVERT: B  515 ARG cc_start: 0.6678 (tpm170) cc_final: 0.6020 (ttt180)
REVERT: B  524 MET cc_start: 0.2418 (ptt) cc_final: 0.1513 (ttt)
REVERT: B  560 ILE cc_start: 0.8607 (tp) cc_final: 0.8250 (tt)
REVERT: B  666 TYR cc_start: 0.3959 (t80) cc_final: 0.3319 (m-80)
  outliers start: 26
  outliers final: 10
  residues processed: 203
  average time/residue: 0.2588
  time to fit residues: 73.6960
Evaluate side-chains
  174 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 HIS
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  446 GLU
Chi-restraints excluded: chain A residue  617 PHE
Chi-restraints excluded: chain A residue  752 ILE
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  268 ILE
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 75 optimal weight:    0.8980
   chunk 121 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 35 optimal weight:   30.0000
   chunk 137 optimal weight:    4.9990
   chunk 118 optimal weight:    8.9990
   chunk 101 optimal weight:    8.9990
   chunk 102 optimal weight:    8.9990
   chunk 131 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN
** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 215 GLN
B 431 GLN
** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.142225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.115104 restraints weight = 18228.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.114769 restraints weight = 14209.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.115179 restraints weight = 12347.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12072  Z= 0.174
  Angle     :  0.651   9.817  16336  Z= 0.335
  Chirality :  0.042   0.154   1796
  Planarity :  0.006   0.076   2044
  Dihedral  :  5.790  71.712   1590
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 18.91 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.22), residues: 1416
  helix:  0.51 (0.17), residues: 848
  sheet: -1.99 (0.87), residues: 32
  loop : -3.21 (0.23), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 427 
 HIS   0.007   0.001   HIS B 402 
 PHE   0.019   0.001   PHE A 696 
 TYR   0.016   0.002   TYR B 251 
 ARG   0.006   0.000   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04709 (  642)
  hydrogen bonds       : angle       4.72425 ( 1902)
  SS BOND              : bond        0.00633 (    8)
  SS BOND              : angle       4.47618 (   16)
  covalent geometry    : bond        0.00397 (12064)
  covalent geometry    : angle       0.63617 (16320)

*********************** 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
  214 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 169
  time to evaluate  : 1.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  381 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6540 (pp)
REVERT: A  446 GLU cc_start: 0.5727 (OUTLIER) cc_final: 0.5523 (tm-30)
REVERT: A  515 ARG cc_start: 0.6762 (tpm170) cc_final: 0.5972 (ttt180)
REVERT: A  524 MET cc_start: 0.2276 (ptt) cc_final: 0.1398 (ttt)
REVERT: A  560 ILE cc_start: 0.8595 (tp) cc_final: 0.8247 (tt)
REVERT: A  731 ASN cc_start: 0.8658 (m-40) cc_final: 0.8421 (m-40)
REVERT: B  381 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6567 (pp)
REVERT: B  418 LEU cc_start: 0.8162 (tt) cc_final: 0.7603 (mp)
REVERT: B  515 ARG cc_start: 0.6703 (tpm170) cc_final: 0.6072 (ttt180)
REVERT: B  524 MET cc_start: 0.2521 (ptt) cc_final: 0.1746 (ttm)
REVERT: B  560 ILE cc_start: 0.8604 (tp) cc_final: 0.8246 (tt)
REVERT: B  666 TYR cc_start: 0.3939 (t80) cc_final: 0.3288 (m-80)
  outliers start: 45
  outliers final: 22
  residues processed: 205
  average time/residue: 0.2546
  time to fit residues: 74.9562
Evaluate side-chains
  189 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 164
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
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  245 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  381 LEU
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  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  245 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  431 GLN
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  752 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 84 optimal weight:    8.9990
   chunk 79 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 20 optimal weight:    5.9990
   chunk 135 optimal weight:    1.9990
   chunk 132 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 125 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN
** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.142968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.115815 restraints weight = 18284.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.115555 restraints weight = 14392.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.115976 restraints weight = 12410.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12072  Z= 0.153
  Angle     :  0.628   9.826  16336  Z= 0.323
  Chirality :  0.042   0.151   1796
  Planarity :  0.005   0.075   2044
  Dihedral  :  5.342  72.634   1587
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 19.84 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.22), residues: 1416
  helix:  0.71 (0.18), residues: 844
  sheet: -1.70 (0.93), residues: 32
  loop : -3.09 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 427 
 HIS   0.008   0.001   HIS B 402 
 PHE   0.025   0.001   PHE A 617 
 TYR   0.017   0.001   TYR A 182 
 ARG   0.006   0.000   ARG A 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04616 (  642)
  hydrogen bonds       : angle       4.68731 ( 1902)
  SS BOND              : bond        0.00534 (    8)
  SS BOND              : angle       4.12064 (   16)
  covalent geometry    : bond        0.00345 (12064)
  covalent geometry    : angle       0.61485 (16320)

*********************** 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
  212 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 176
  time to evaluate  : 1.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 LEU cc_start: 0.8143 (tt) cc_final: 0.7695 (mp)
REVERT: A  491 PHE cc_start: 0.4962 (t80) cc_final: 0.4746 (t80)
REVERT: A  515 ARG cc_start: 0.6772 (tpm170) cc_final: 0.5974 (ttt180)
REVERT: A  524 MET cc_start: 0.2279 (ptt) cc_final: 0.1589 (ttt)
REVERT: A  560 ILE cc_start: 0.8578 (tp) cc_final: 0.8259 (tt)
REVERT: A  731 ASN cc_start: 0.8675 (m-40) cc_final: 0.8417 (m-40)
REVERT: B  381 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6648 (pp)
REVERT: B  418 LEU cc_start: 0.8132 (tt) cc_final: 0.7581 (mp)
REVERT: B  515 ARG cc_start: 0.6723 (tpm170) cc_final: 0.6052 (ttt180)
REVERT: B  524 MET cc_start: 0.2507 (ptt) cc_final: 0.1627 (ttt)
REVERT: B  560 ILE cc_start: 0.8601 (tp) cc_final: 0.8243 (tt)
REVERT: B  666 TYR cc_start: 0.3796 (t80) cc_final: 0.3140 (m-80)
  outliers start: 36
  outliers final: 25
  residues processed: 203
  average time/residue: 0.2572
  time to fit residues: 73.0566
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  : 1.337 
-------------------------------------------------------------------------------
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  245 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  773 ILE
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  268 ILE
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  395 CYS
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  622 MET
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  773 ILE
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 59 optimal weight:    0.9990
   chunk 128 optimal weight:    1.9990
   chunk 111 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0870
   chunk 46 optimal weight:    0.2980
   chunk 124 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6160

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

Flipped N/Q/H residues before XYZ refinement:
** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.146624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.120152 restraints weight = 18309.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.119762 restraints weight = 13835.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.120266 restraints weight = 11651.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12072  Z= 0.127
  Angle     :  0.611   9.847  16336  Z= 0.314
  Chirality :  0.040   0.150   1796
  Planarity :  0.005   0.076   2044
  Dihedral  :  4.804  21.139   1584
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 20.94 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.22), residues: 1416
  helix:  0.94 (0.18), residues: 842
  sheet: -1.43 (0.98), residues: 32
  loop : -2.91 (0.24), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 427 
 HIS   0.007   0.001   HIS B 402 
 PHE   0.013   0.001   PHE B 589 
 TYR   0.015   0.001   TYR A 182 
 ARG   0.012   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04323 (  642)
  hydrogen bonds       : angle       4.59300 ( 1902)
  SS BOND              : bond        0.00552 (    8)
  SS BOND              : angle       3.92025 (   16)
  covalent geometry    : bond        0.00272 (12064)
  covalent geometry    : angle       0.59928 (16320)

*********************** 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
  216 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 1.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 LEU cc_start: 0.8035 (tt) cc_final: 0.7610 (mp)
REVERT: A  491 PHE cc_start: 0.5001 (t80) cc_final: 0.4759 (t80)
REVERT: A  515 ARG cc_start: 0.6809 (tpm170) cc_final: 0.6005 (ttt180)
REVERT: A  524 MET cc_start: 0.2390 (ptt) cc_final: 0.1790 (ttt)
REVERT: A  560 ILE cc_start: 0.8568 (tp) cc_final: 0.8211 (tt)
REVERT: A  706 MET cc_start: 0.8704 (mmp) cc_final: 0.8313 (mmp)
REVERT: A  731 ASN cc_start: 0.8577 (m-40) cc_final: 0.8165 (m-40)
REVERT: B  418 LEU cc_start: 0.8062 (tt) cc_final: 0.7637 (mp)
REVERT: B  515 ARG cc_start: 0.6724 (tpm170) cc_final: 0.6059 (ttt180)
REVERT: B  524 MET cc_start: 0.2296 (ptt) cc_final: 0.1575 (ttt)
REVERT: B  560 ILE cc_start: 0.8590 (tp) cc_final: 0.8190 (tt)
REVERT: B  706 MET cc_start: 0.8731 (mmp) cc_final: 0.8346 (mmt)
  outliers start: 32
  outliers final: 21
  residues processed: 208
  average time/residue: 0.2548
  time to fit residues: 73.7972
Evaluate side-chains
  183 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 162
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  220 LEU
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  752 ILE
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  395 CYS
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  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 8 optimal weight:    6.9990
   chunk 113 optimal weight:    5.9990
   chunk 125 optimal weight:    0.9980
   chunk 13 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 99 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 115 optimal weight:    8.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
B 431 GLN
** B 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.144325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.117663 restraints weight = 18434.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.117141 restraints weight = 14172.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.117876 restraints weight = 12184.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12072  Z= 0.156
  Angle     :  0.647   9.696  16336  Z= 0.333
  Chirality :  0.042   0.159   1796
  Planarity :  0.005   0.074   2044
  Dihedral  :  4.882  28.319   1584
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 21.56 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.22), residues: 1416
  helix:  0.95 (0.18), residues: 844
  sheet: -1.16 (0.99), residues: 32
  loop : -2.84 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 427 
 HIS   0.007   0.001   HIS B 402 
 PHE   0.015   0.001   PHE B 617 
 TYR   0.020   0.001   TYR B 182 
 ARG   0.004   0.000   ARG B 125 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04526 (  642)
  hydrogen bonds       : angle       4.60430 ( 1902)
  SS BOND              : bond        0.00627 (    8)
  SS BOND              : angle       4.60544 (   16)
  covalent geometry    : bond        0.00359 (12064)
  covalent geometry    : angle       0.63107 (16320)

*********************** 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
  198 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 164
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
REVERT: A  418 LEU cc_start: 0.8136 (tt) cc_final: 0.7701 (mp)
REVERT: A  491 PHE cc_start: 0.5140 (t80) cc_final: 0.4924 (t80)
REVERT: A  515 ARG cc_start: 0.6828 (tpm170) cc_final: 0.6053 (ttt180)
REVERT: A  524 MET cc_start: 0.2381 (ptt) cc_final: 0.1809 (ttt)
REVERT: A  560 ILE cc_start: 0.8581 (tp) cc_final: 0.8208 (tt)
REVERT: A  706 MET cc_start: 0.8730 (mmp) cc_final: 0.8342 (mmt)
REVERT: A  731 ASN cc_start: 0.8590 (m-40) cc_final: 0.8286 (m-40)
REVERT: B  418 LEU cc_start: 0.8182 (tt) cc_final: 0.7708 (mp)
REVERT: B  515 ARG cc_start: 0.6750 (tpm170) cc_final: 0.6049 (ttt180)
REVERT: B  524 MET cc_start: 0.2250 (ptt) cc_final: 0.1544 (ttt)
REVERT: B  560 ILE cc_start: 0.8572 (tp) cc_final: 0.8186 (tt)
  outliers start: 34
  outliers final: 28
  residues processed: 190
  average time/residue: 0.2627
  time to fit residues: 70.3022
Evaluate side-chains
  185 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 1.252 
-------------------------------------------------------------------------------
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  245 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  773 ILE
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  431 GLN
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  773 ILE
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 40 optimal weight:    5.9990
   chunk 131 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 80 optimal weight:    0.1980
   chunk 121 optimal weight:    9.9990
   chunk 135 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 129 optimal weight:    1.9990
   chunk 138 optimal weight:    1.9990
   chunk 98 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.145275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.118108 restraints weight = 18377.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.117526 restraints weight = 14922.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.118141 restraints weight = 13334.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12072  Z= 0.144
  Angle     :  0.657  14.399  16336  Z= 0.330
  Chirality :  0.042   0.150   1796
  Planarity :  0.005   0.074   2044
  Dihedral  :  4.835  26.723   1584
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 22.19 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.22), residues: 1416
  helix:  1.00 (0.18), residues: 844
  sheet: -0.80 (1.04), residues: 32
  loop : -2.79 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 427 
 HIS   0.006   0.001   HIS B 402 
 PHE   0.035   0.001   PHE A 617 
 TYR   0.018   0.001   TYR B 182 
 ARG   0.013   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04481 (  642)
  hydrogen bonds       : angle       4.62939 ( 1902)
  SS BOND              : bond        0.00553 (    8)
  SS BOND              : angle       4.12137 (   16)
  covalent geometry    : bond        0.00328 (12064)
  covalent geometry    : angle       0.64442 (16320)

*********************** 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
  198 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 162
  time to evaluate  : 1.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7655 (t80)
REVERT: A  418 LEU cc_start: 0.8122 (tt) cc_final: 0.7699 (mp)
REVERT: A  491 PHE cc_start: 0.5103 (t80) cc_final: 0.4901 (t80)
REVERT: A  515 ARG cc_start: 0.6832 (tpm170) cc_final: 0.6070 (ttt180)
REVERT: A  524 MET cc_start: 0.2333 (ptt) cc_final: 0.1784 (ttt)
REVERT: A  560 ILE cc_start: 0.8569 (tp) cc_final: 0.8201 (tt)
REVERT: A  706 MET cc_start: 0.8691 (mmp) cc_final: 0.8274 (mmt)
REVERT: A  731 ASN cc_start: 0.8577 (m-40) cc_final: 0.8272 (m-40)
REVERT: B  418 LEU cc_start: 0.8147 (tt) cc_final: 0.7686 (mp)
REVERT: B  515 ARG cc_start: 0.6795 (tpm170) cc_final: 0.6133 (ttt180)
REVERT: B  524 MET cc_start: 0.2185 (ptt) cc_final: 0.1511 (ttt)
REVERT: B  560 ILE cc_start: 0.8556 (tp) cc_final: 0.8171 (tt)
  outliers start: 36
  outliers final: 26
  residues processed: 188
  average time/residue: 0.2606
  time to fit residues: 68.5229
Evaluate side-chains
  186 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
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  245 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  773 ILE
Chi-restraints excluded: chain A residue  829 LEU
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  245 THR
Chi-restraints excluded: chain B residue  268 ILE
Chi-restraints excluded: chain B residue  352 VAL
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  538 VAL
Chi-restraints excluded: chain B residue  752 ILE
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 70 optimal weight:   10.0000
   chunk 15 optimal weight:    0.0870
   chunk 89 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9980
   chunk 119 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 141 optimal weight:    7.9990
   chunk 65 optimal weight:    0.0010
   overall best weight:    0.8168

-------------------------------------------------------------------------------
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 = 0.3987 r_free = 0.3987 target = 0.146748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.120431 restraints weight = 18288.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.119747 restraints weight = 14133.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.120799 restraints weight = 11803.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12072  Z= 0.131
  Angle     :  0.655  13.840  16336  Z= 0.327
  Chirality :  0.041   0.233   1796
  Planarity :  0.005   0.075   2044
  Dihedral  :  4.759  24.571   1584
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 23.28 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.22), residues: 1416
  helix:  1.10 (0.18), residues: 844
  sheet: -0.66 (1.05), residues: 32
  loop : -2.67 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 427 
 HIS   0.005   0.001   HIS B 402 
 PHE   0.028   0.001   PHE A 617 
 TYR   0.016   0.001   TYR B 277 
 ARG   0.013   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04348 (  642)
  hydrogen bonds       : angle       4.58624 ( 1902)
  SS BOND              : bond        0.00459 (    8)
  SS BOND              : angle       3.78841 (   16)
  covalent geometry    : bond        0.00288 (12064)
  covalent geometry    : angle       0.64442 (16320)

*********************** 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
  194 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7624 (t80)
REVERT: A  418 LEU cc_start: 0.8030 (tt) cc_final: 0.7593 (mp)
REVERT: A  491 PHE cc_start: 0.4994 (t80) cc_final: 0.4762 (t80)
REVERT: A  515 ARG cc_start: 0.6817 (tpm170) cc_final: 0.6079 (ttt180)
REVERT: A  524 MET cc_start: 0.2309 (ptt) cc_final: 0.1736 (ttt)
REVERT: A  560 ILE cc_start: 0.8577 (tp) cc_final: 0.8196 (tt)
REVERT: A  706 MET cc_start: 0.8700 (mmp) cc_final: 0.8320 (mmt)
REVERT: A  731 ASN cc_start: 0.8538 (m-40) cc_final: 0.8265 (m-40)
REVERT: B  418 LEU cc_start: 0.8058 (tt) cc_final: 0.7626 (mp)
REVERT: B  515 ARG cc_start: 0.6792 (tpm170) cc_final: 0.6135 (ttt180)
REVERT: B  524 MET cc_start: 0.2115 (ptt) cc_final: 0.1545 (ttt)
REVERT: B  560 ILE cc_start: 0.8551 (tp) cc_final: 0.8162 (tt)
REVERT: B  706 MET cc_start: 0.8763 (mmp) cc_final: 0.8311 (mmt)
  outliers start: 28
  outliers final: 24
  residues processed: 187
  average time/residue: 0.2699
  time to fit residues: 70.6763
Evaluate side-chains
  182 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  245 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  849 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  538 VAL
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  773 ILE
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 41 optimal weight:    1.9990
   chunk 137 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9980
   chunk 135 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 138 optimal weight:    0.6980
   chunk 73 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3976 r_free = 0.3976 target = 0.145899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.118687 restraints weight = 17970.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.118598 restraints weight = 13583.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.118923 restraints weight = 12210.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12072  Z= 0.145
  Angle     :  0.666  14.405  16336  Z= 0.334
  Chirality :  0.042   0.182   1796
  Planarity :  0.005   0.074   2044
  Dihedral  :  4.748  24.304   1584
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 23.28 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.23), residues: 1416
  helix:  1.11 (0.18), residues: 844
  sheet: -0.66 (1.05), residues: 32
  loop : -2.65 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 427 
 HIS   0.005   0.001   HIS B 402 
 PHE   0.030   0.001   PHE A 617 
 TYR   0.018   0.001   TYR B 323 
 ARG   0.012   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04421 (  642)
  hydrogen bonds       : angle       4.59551 ( 1902)
  SS BOND              : bond        0.00484 (    8)
  SS BOND              : angle       3.84390 (   16)
  covalent geometry    : bond        0.00330 (12064)
  covalent geometry    : angle       0.65493 (16320)

********************** 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
  191 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 159
  time to evaluate  : 1.389 
Fit side-chains
   revert: symmetry clash
REVERT: A  418 LEU cc_start: 0.8109 (tt) cc_final: 0.7661 (mp)
REVERT: A  515 ARG cc_start: 0.6826 (tpm170) cc_final: 0.6126 (ttt180)
REVERT: A  524 MET cc_start: 0.2500 (ptt) cc_final: 0.1899 (ttt)
REVERT: A  560 ILE cc_start: 0.8571 (tp) cc_final: 0.8171 (tt)
REVERT: A  706 MET cc_start: 0.8697 (mmp) cc_final: 0.8325 (mmt)
REVERT: A  731 ASN cc_start: 0.8493 (m-40) cc_final: 0.8230 (m-40)
REVERT: B  391 MET cc_start: 0.8459 (tpp) cc_final: 0.8179 (tpp)
REVERT: B  418 LEU cc_start: 0.8126 (tt) cc_final: 0.7703 (mp)
REVERT: B  515 ARG cc_start: 0.6827 (tpm170) cc_final: 0.6174 (ttt180)
REVERT: B  524 MET cc_start: 0.2314 (ptt) cc_final: 0.1685 (ttt)
REVERT: B  560 ILE cc_start: 0.8554 (tp) cc_final: 0.8166 (tt)
REVERT: B  706 MET cc_start: 0.8756 (mmp) cc_final: 0.8370 (mmt)
REVERT: B  755 LYS cc_start: 0.6929 (mptt) cc_final: 0.6591 (tptt)
  outliers start: 32
  outliers final: 25
  residues processed: 182
  average time/residue: 0.2588
  time to fit residues: 66.2854
Evaluate side-chains
  182 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 157
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  245 THR
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  395 CYS
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  752 ILE
Chi-restraints excluded: chain A residue  829 LEU
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  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  432 MET
Chi-restraints excluded: chain B residue  538 VAL
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  773 ILE
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 5 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0970
   chunk 51 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 83 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 546 ASN
B 431 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.147820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.120550 restraints weight = 18112.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.120203 restraints weight = 14219.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.120651 restraints weight = 12359.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12072  Z= 0.130
  Angle     :  0.646  13.610  16336  Z= 0.324
  Chirality :  0.041   0.147   1796
  Planarity :  0.006   0.075   2044
  Dihedral  :  4.676  23.948   1584
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 24.14 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.23), residues: 1416
  helix:  1.15 (0.18), residues: 852
  sheet: -0.59 (1.05), residues: 32
  loop : -2.65 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 427 
 HIS   0.004   0.001   HIS B 402 
 PHE   0.030   0.001   PHE A 617 
 TYR   0.018   0.001   TYR B 323 
 ARG   0.012   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04322 (  642)
  hydrogen bonds       : angle       4.56405 ( 1902)
  SS BOND              : bond        0.00463 (    8)
  SS BOND              : angle       3.53424 (   16)
  covalent geometry    : bond        0.00285 (12064)
  covalent geometry    : angle       0.63703 (16320)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3947.92 seconds
wall clock time: 70 minutes 18.45 seconds (4218.45 seconds total)