Starting phenix.real_space_refine
on Sun Apr  5 12:37:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w1b_65525/04_2026/9w1b_65525.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w1b_65525/04_2026/9w1b_65525.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w1b_65525/04_2026/9w1b_65525.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w1b_65525/04_2026/9w1b_65525.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w1b_65525/04_2026/9w1b_65525.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w1b_65525/04_2026/9w1b_65525.map"
  }
  resolution = 2.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.078
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
     P      32      5.49       5
     S      44      5.16       5
     C    6724      2.51       5
     N    1626      2.21       5
     O    1768      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10194
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4843
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 17, 'TRANS': 554}
          Chain breaks: 3
    Chain: "E"
      Number of atoms: 4843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4843
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 17, 'TRANS': 554}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 290
          Unusual residues: {'8PE': 1, 'IHP': 3, 'PO4': 3, 'POV': 9}
          Classifications: {'undetermined': 16}
          Link IDs: {None: 15}
          Unresolved non-hydrogen bonds: 348
          Unresolved non-hydrogen angles: 420
          Unresolved non-hydrogen dihedrals: 312
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-3': 9}
          Unresolved non-hydrogen planarities: 38
    Chain: "E"
      Number of atoms: 218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 218
          Unusual residues: {'8PE': 1, 'IHP': 1, 'PO4': 3, 'POV': 9}
          Classifications: {'undetermined': 14}
          Link IDs: {None: 13}
          Unresolved non-hydrogen bonds: 348
          Unresolved non-hydrogen angles: 420
          Unresolved non-hydrogen dihedrals: 312
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'POV:plan-3': 9, 'POV:plan-1': 2}
          Unresolved non-hydrogen planarities: 38
  Time building chain proxies: 2.24, per 1000 atoms: 0.22
  Number of scatterers: 10194
  At special positions: 0
  Unit cell: (96.743, 111.961, 98.917, 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)
     S      44     16.00
     P      32     15.00
     O    1768      8.00
     N    1626      7.00
     C    6724      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 448 " - pdb=" SG  CYS A 460 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 448 " - pdb=" SG  CYS E 460 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 487.2 milliseconds
  

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2204

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 2 sheets defined
      76.0% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 33
      removed outlier: 3.583A  pdb=" N   GLY A  25 " --> pdb=" O   ASP A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 111
      removed outlier: 3.695A  pdb=" N   GLN A  69 " --> pdb=" O   HIS A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 209
    Processing helix  chain 'A' and resid 213 through 223
      removed outlier: 3.520A  pdb=" N   TRP A 217 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ARG A 223 " --> pdb=" O   ASP A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 248
    Processing helix  chain 'A' and resid 251 through 260
    Processing helix  chain 'A' and resid 268 through 291
      Proline residue:  A 284  - end of helix
      removed outlier: 3.532A  pdb=" N   CYS A 291 " --> pdb=" O   ILE A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 329
      removed outlier: 3.699A  pdb=" N   TYR A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 337
      removed outlier: 3.711A  pdb=" N   ILE A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 370
      removed outlier: 3.548A  pdb=" N   HIS A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 394
    Processing helix  chain 'A' and resid 400 through 416
      removed outlier: 3.617A  pdb=" N   ARG A 404 " --> pdb=" O   TYR A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 435
      removed outlier: 3.530A  pdb=" N   SER A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 452
      removed outlier: 3.826A  pdb=" N   LEU A 445 " --> pdb=" O   GLY A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 460
    Processing helix  chain 'A' and resid 466 through 491
      Proline residue:  A 475  - end of helix
    Processing helix  chain 'A' and resid 493 through 519
    Processing helix  chain 'A' and resid 521 through 547
      removed outlier: 3.632A  pdb=" N   ARG A 525 " --> pdb=" O   GLY A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 583
    Processing helix  chain 'A' and resid 586 through 592
      removed outlier: 3.838A  pdb=" N   CYS A 590 " --> pdb=" O   PHE A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 636
      removed outlier: 4.197A  pdb=" N   PHE A 604 " --> pdb=" O   SER A 600 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 21 through 33
      removed outlier: 3.583A  pdb=" N   GLY E  25 " --> pdb=" O   ASP E  21 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 111
      removed outlier: 3.695A  pdb=" N   GLN E  69 " --> pdb=" O   HIS E  65 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 166 through 209
    Processing helix  chain 'E' and resid 213 through 223
      removed outlier: 3.520A  pdb=" N   TRP E 217 " --> pdb=" O   LEU E 213 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ARG E 223 " --> pdb=" O   ASP E 219 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 230 through 248
    Processing helix  chain 'E' and resid 251 through 260
    Processing helix  chain 'E' and resid 268 through 291
      Proline residue:  E 284  - end of helix
      removed outlier: 3.532A  pdb=" N   CYS E 291 " --> pdb=" O   ILE E 287 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 296 through 329
      removed outlier: 3.699A  pdb=" N   TYR E 301 " --> pdb=" O   GLU E 297 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 332 through 337
      removed outlier: 3.711A  pdb=" N   ILE E 336 " --> pdb=" O   ASN E 332 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 346 through 370
      removed outlier: 3.548A  pdb=" N   HIS E 350 " --> pdb=" O   ASN E 346 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 379 through 394
    Processing helix  chain 'E' and resid 400 through 416
      removed outlier: 3.617A  pdb=" N   ARG E 404 " --> pdb=" O   TYR E 400 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 423 through 435
      removed outlier: 3.530A  pdb=" N   SER E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 441 through 452
      removed outlier: 3.826A  pdb=" N   LEU E 445 " --> pdb=" O   GLY E 441 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 456 through 460
    Processing helix  chain 'E' and resid 466 through 491
      Proline residue:  E 475  - end of helix
    Processing helix  chain 'E' and resid 493 through 519
    Processing helix  chain 'E' and resid 521 through 547
      removed outlier: 3.632A  pdb=" N   ARG E 525 " --> pdb=" O   GLY E 521 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 569 through 583
    Processing helix  chain 'E' and resid 586 through 592
      removed outlier: 3.839A  pdb=" N   CYS E 590 " --> pdb=" O   PHE E 586 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 600 through 636
      removed outlier: 4.197A  pdb=" N   PHE E 604 " --> pdb=" O   SER E 600 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 551 through 553
    Processing sheet with id=AA2, first strand: chain 'E' and resid 551 through 553

    668 hydrogen bonds defined for protein.
    1992 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.18

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2551
        1.33 -     1.46: 2308
        1.46 -     1.58: 5507
        1.58 -     1.70: 28
        1.70 -     1.82: 70
  Bond restraints: 10464
  Sorted by residual:
  bond pdb=" CA  HIS A  65 "
       pdb=" C   HIS A  65 "
    ideal  model  delta    sigma   weight residual
    1.524  1.414  0.110 1.26e-02 6.30e+03 7.58e+01
  bond pdb=" CA  HIS E  65 "
       pdb=" C   HIS E  65 "
    ideal  model  delta    sigma   weight residual
    1.524  1.414  0.110 1.26e-02 6.30e+03 7.57e+01
  bond pdb=" C21 POV E 704 "
       pdb=" O21 POV E 704 "
    ideal  model  delta    sigma   weight residual
    1.330  1.454 -0.124 2.00e-02 2.50e+03 3.85e+01
  bond pdb=" C21 POV A 702 "
       pdb=" O21 POV A 702 "
    ideal  model  delta    sigma   weight residual
    1.330  1.454 -0.124 2.00e-02 2.50e+03 3.85e+01
  bond pdb=" C21 POV E 706 "
       pdb=" O21 POV E 706 "
    ideal  model  delta    sigma   weight residual
    1.330  1.454 -0.124 2.00e-02 2.50e+03 3.84e+01
  ... (remaining 10459 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.17: 13998
        5.17 -    10.35: 92
       10.35 -    15.52: 0
       15.52 -    20.70: 0
       20.70 -    25.87: 2
  Bond angle restraints: 14092
  Sorted by residual:
  angle pdb=" N   HIS E  65 "
        pdb=" CA  HIS E  65 "
        pdb=" C   HIS E  65 "
      ideal   model   delta    sigma   weight residual
     109.81   83.94   25.87 2.21e+00 2.05e-01 1.37e+02
  angle pdb=" N   HIS A  65 "
        pdb=" CA  HIS A  65 "
        pdb=" C   HIS A  65 "
      ideal   model   delta    sigma   weight residual
     109.81   83.94   25.87 2.21e+00 2.05e-01 1.37e+02
  angle pdb=" N   ARG A  63 "
        pdb=" CA  ARG A  63 "
        pdb=" C   ARG A  63 "
      ideal   model   delta    sigma   weight residual
     109.07  118.52   -9.45 1.61e+00 3.86e-01 3.44e+01
  angle pdb=" N   ARG E  63 "
        pdb=" CA  ARG E  63 "
        pdb=" C   ARG E  63 "
      ideal   model   delta    sigma   weight residual
     109.07  118.52   -9.45 1.61e+00 3.86e-01 3.44e+01
  angle pdb=" O   HIS E  65 "
        pdb=" C   HIS E  65 "
        pdb=" N   PRO E  66 "
      ideal   model   delta    sigma   weight residual
     121.32  125.73   -4.41 1.15e+00 7.56e-01 1.47e+01
  ... (remaining 14087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.93: 5754
       33.93 -    67.85: 362
       67.85 -   101.78: 54
      101.78 -   135.71: 26
      135.71 -   169.63: 4
  Dihedral angle restraints: 6200
    sinusoidal: 2798
      harmonic: 3402
  Sorted by residual:
  dihedral pdb=" CA  LEU A 453 "
           pdb=" C   LEU A 453 "
           pdb=" N   TRP A 454 "
           pdb=" CA  TRP A 454 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -136.55  -43.45     0      5.00e+00 4.00e-02 7.55e+01
  dihedral pdb=" CA  LEU E 453 "
           pdb=" C   LEU E 453 "
           pdb=" N   TRP E 454 "
           pdb=" CA  TRP E 454 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.57  -43.43     0      5.00e+00 4.00e-02 7.55e+01
  dihedral pdb=" N   HIS A  65 "
           pdb=" C   HIS A  65 "
           pdb=" CA  HIS A  65 "
           pdb=" CB  HIS A  65 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  109.56   13.24     0      2.50e+00 1.60e-01 2.80e+01
  ... (remaining 6197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.999: 1432
       0.999 -    1.998: 0
       1.998 -    2.997: 0
       2.997 -    3.996: 0
       3.996 -    4.995: 16
  Chirality restraints: 1448
  Sorted by residual:
  chirality pdb=" C2  IHP A 715 "
            pdb=" C1  IHP A 715 "
            pdb=" C3  IHP A 715 "
            pdb=" O12 IHP A 715 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    2.48   -4.99 2.00e-01 2.50e+01 6.24e+02
  chirality pdb=" C2  IHP A 710 "
            pdb=" C1  IHP A 710 "
            pdb=" C3  IHP A 710 "
            pdb=" O12 IHP A 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    2.48   -4.99 2.00e-01 2.50e+01 6.24e+02
  chirality pdb=" C2  IHP E 702 "
            pdb=" C1  IHP E 702 "
            pdb=" C3  IHP E 702 "
            pdb=" O12 IHP E 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    2.46   -4.98 2.00e-01 2.50e+01 6.21e+02
  ... (remaining 1445 not shown)

  Planarity restraints: 1710
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS E  65 "   -0.041 5.00e-02 4.00e+02   6.24e-02 6.22e+00
        pdb=" N   PRO E  66 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO E  66 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E  66 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A  65 "   -0.041 5.00e-02 4.00e+02   6.24e-02 6.22e+00
        pdb=" N   PRO A  66 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  63 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.14e+00
        pdb=" C   ARG A  63 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ARG A  63 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PHE A  64 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1707 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1067
        2.74 -     3.28: 9608
        3.28 -     3.82: 16582
        3.82 -     4.36: 19575
        4.36 -     4.90: 34132
  Nonbonded interactions: 80964
  Sorted by model distance:
  nonbonded pdb=" O   HIS A  65 "
            pdb=" N   LEU A  67 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   HIS E  65 "
            pdb=" N   LEU E  67 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   HIS A  65 "
            pdb=" N   PHE A  68 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" O   HIS E  65 "
            pdb=" N   PHE E  68 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" O11 IHP A 710 "
            pdb=" O12 IHP A 710 "
     model   vdw
     2.430 2.432
  ... (remaining 80959 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 9 through 701 or (resid 703 and (name C21 or name C22 or n \ 
ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29  \ 
or name O21 or name O22 or name C210)) or (resid 704 and (name C21 or name C22 o \ 
r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 
29 or name O21 or name O22 or name C210 or name C211 or name C212)) or resid 706 \ 
 or (resid 708 and (name C21 or name C22 or name C23 or name C24 or name C25 or  \ 
name C26 or name C27 or name C28 or name C29 or name O21 or name O22 or name C21 \ 
0 or name C211 or name C212)) or resid 709 or resid 712 through 713))
  selection = (chain 'E' and (resid 9 through 640 or (resid 701 and (name C21 or name C22 or n \ 
ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29  \ 
or name O21 or name O22 or name C210)) or resid 703 through 704 or (resid 706 an \ 
d (name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name  \ 
C27 or name C28 or name C29 or name O21 or name O22 or name C210 or name C211 or \ 
 name C212)) or resid 708 or (resid 709 and (name C21 or name C22 or name C23 or \ 
 name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name O2 \ 
1 or name O22 or name C210)) or resid 712 through 713))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.530
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
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      :  0.009   0.124  10466  Z= 0.473
  Angle     :  1.090  25.871  14096  Z= 0.512
  Chirality :  0.512   4.995   1448
  Planarity :  0.005   0.062   1710
  Dihedral  : 23.776 169.634   3990
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.96 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 28.28 %
    Favored  : 68.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.25), residues: 1128
  helix:  2.17 (0.17), residues: 814
  sheet:  None (None), residues: 0
  loop : -3.30 (0.29), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 199 
 TYR   0.015   0.002   TYR E 301 
 PHE   0.023   0.002   PHE A 275 
 TRP   0.015   0.002   TRP E 454 
 HIS   0.011   0.001   HIS E  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00904 (10464)
  covalent geometry    : angle       1.08967 (14092)
  SS BOND              : bond        0.00650 (    2)
  SS BOND              : angle       1.90176 (    4)
  hydrogen bonds       : bond        0.13514 (  668)
  hydrogen bonds       : angle       4.83422 ( 1992)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 101
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A   84 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7387 (mp0)
REVERT: A  100 GLN cc_start: 0.8241 (mt0) cc_final: 0.7945 (mt0)
REVERT: A  106 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7378 (ttmt)
REVERT: A  200 LYS cc_start: 0.7604 (tptp) cc_final: 0.6817 (mtmt)
REVERT: A  233 THR cc_start: 0.7676 (p) cc_final: 0.7426 (t)
REVERT: A  343 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7258 (mttp)
REVERT: A  504 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8407 (mp)
REVERT: A  546 MET cc_start: 0.9240 (mmt) cc_final: 0.9006 (mmt)
REVERT: A  583 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7912 (mtt90)
REVERT: A  623 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8302 (tm-30)
REVERT: E   84 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7334 (mp0)
REVERT: E  100 GLN cc_start: 0.8269 (mt0) cc_final: 0.7958 (mt0)
REVERT: E  106 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7379 (ttmt)
REVERT: E  200 LYS cc_start: 0.7602 (tptp) cc_final: 0.6815 (mtmt)
REVERT: E  233 THR cc_start: 0.7680 (p) cc_final: 0.7418 (t)
REVERT: E  402 ARG cc_start: 0.7733 (mtt-85) cc_final: 0.7143 (mtp180)
REVERT: E  504 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8397 (mp)
REVERT: E  546 MET cc_start: 0.9244 (mmt) cc_final: 0.8805 (tpp)
REVERT: E  583 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7933 (mtt90)
  outliers start: 38
  outliers final: 18
  residues processed: 139
  average time/residue: 0.6669
  time to fit residues: 98.5041
Evaluate side-chains
  126 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   84 GLU
Chi-restraints excluded: chain A residue  106 LYS
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  265 LYS
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  548 TRP
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain A residue  623 GLU
Chi-restraints excluded: chain A residue  640 LYS
Chi-restraints excluded: chain E residue   19 TYR
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   84 GLU
Chi-restraints excluded: chain E residue  106 LYS
Chi-restraints excluded: chain E residue  173 LEU
Chi-restraints excluded: chain E residue  265 LYS
Chi-restraints excluded: chain E residue  396 VAL
Chi-restraints excluded: chain E residue  398 VAL
Chi-restraints excluded: chain E residue  504 ILE
Chi-restraints excluded: chain E residue  518 ILE
Chi-restraints excluded: chain E residue  548 TRP
Chi-restraints excluded: chain E residue  583 ARG
Chi-restraints excluded: chain E residue  640 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.1980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.3980
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS
A 425 GLN
A 595 HIS
E  62 HIS
E  74 GLN
E 425 GLN
E 595 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.161045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.126736 restraints weight = 11991.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.65
r_work: 0.3376 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.0968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10466  Z= 0.161
  Angle     :  0.839  15.757  14096  Z= 0.359
  Chirality :  0.053   0.575   1448
  Planarity :  0.004   0.048   1710
  Dihedral  : 16.462  96.787   1757
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 26.16 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.25), residues: 1128
  helix:  2.55 (0.17), residues: 830
  sheet:  None (None), residues: 0
  loop : -3.08 (0.31), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  63 
 TYR   0.012   0.001   TYR E 528 
 PHE   0.022   0.001   PHE A 275 
 TRP   0.011   0.001   TRP E 454 
 HIS   0.004   0.001   HIS E 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (10464)
  covalent geometry    : angle       0.83880 (14092)
  SS BOND              : bond        0.00551 (    2)
  SS BOND              : angle       1.61626 (    4)
  hydrogen bonds       : bond        0.07002 (  668)
  hydrogen bonds       : angle       3.98008 ( 1992)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 114
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  100 GLN cc_start: 0.8241 (mt0) cc_final: 0.7970 (mt0)
REVERT: A  200 LYS cc_start: 0.7290 (tptp) cc_final: 0.6741 (mtmt)
REVERT: A  233 THR cc_start: 0.7590 (p) cc_final: 0.7324 (t)
REVERT: A  267 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.7085 (p90)
REVERT: A  341 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7653 (mm-40)
REVERT: A  342 ARG cc_start: 0.8585 (mtp180) cc_final: 0.8305 (mtp-110)
REVERT: A  343 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7648 (mttp)
REVERT: A  455 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.7177 (mtt-85)
REVERT: A  504 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8452 (mp)
REVERT: A  523 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7202 (ttmm)
REVERT: A  583 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7699 (mtt90)
REVERT: A  637 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7218 (ttm170)
REVERT: E  100 GLN cc_start: 0.8229 (mt0) cc_final: 0.7987 (mt0)
REVERT: E  200 LYS cc_start: 0.7213 (tptp) cc_final: 0.6656 (mtmt)
REVERT: E  233 THR cc_start: 0.7592 (p) cc_final: 0.7331 (t)
REVERT: E  267 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.7062 (p90)
REVERT: E  342 ARG cc_start: 0.8604 (mtp180) cc_final: 0.8257 (mtp-110)
REVERT: E  455 ARG cc_start: 0.7544 (mtm-85) cc_final: 0.7233 (mtt-85)
REVERT: E  504 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8452 (mp)
REVERT: E  523 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7237 (ttmm)
REVERT: E  583 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7720 (mtt90)
REVERT: E  637 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7176 (ttm170)
  outliers start: 55
  outliers final: 11
  residues processed: 156
  average time/residue: 0.6334
  time to fit residues: 105.5501
Evaluate side-chains
  125 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  267 HIS
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  523 LYS
Chi-restraints excluded: chain A residue  548 TRP
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain A residue  637 ARG
Chi-restraints excluded: chain E residue   19 TYR
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue  267 HIS
Chi-restraints excluded: chain E residue  396 VAL
Chi-restraints excluded: chain E residue  431 ASP
Chi-restraints excluded: chain E residue  504 ILE
Chi-restraints excluded: chain E residue  523 LYS
Chi-restraints excluded: chain E residue  548 TRP
Chi-restraints excluded: chain E residue  583 ARG
Chi-restraints excluded: chain E residue  637 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 96 optimal weight:    0.0770
   chunk 91 optimal weight:    1.9990
   chunk 111 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
A 249 ASN
A 595 HIS
E  69 GLN
E 249 ASN
E 595 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.159668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.125142 restraints weight = 11925.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.64
r_work: 0.3365 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10466  Z= 0.163
  Angle     :  0.717  11.748  14096  Z= 0.328
  Chirality :  0.047   0.445   1448
  Planarity :  0.004   0.048   1710
  Dihedral  : 15.240  73.248   1710
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 25.97 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.25), residues: 1128
  helix:  2.50 (0.17), residues: 844
  sheet:  None (None), residues: 0
  loop : -2.91 (0.32), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 199 
 TYR   0.012   0.002   TYR E 528 
 PHE   0.023   0.001   PHE A 275 
 TRP   0.009   0.001   TRP A 347 
 HIS   0.004   0.001   HIS A 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10464)
  covalent geometry    : angle       0.71683 (14092)
  SS BOND              : bond        0.00605 (    2)
  SS BOND              : angle       1.77517 (    4)
  hydrogen bonds       : bond        0.07125 (  668)
  hydrogen bonds       : angle       3.85021 ( 1992)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 108
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   84 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7355 (mp0)
REVERT: A  100 GLN cc_start: 0.8319 (mt0) cc_final: 0.8056 (mt0)
REVERT: A  200 LYS cc_start: 0.7170 (tptp) cc_final: 0.6643 (ttmt)
REVERT: A  233 THR cc_start: 0.7620 (p) cc_final: 0.7375 (t)
REVERT: A  267 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.7138 (p90)
REVERT: A  341 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7666 (mm-40)
REVERT: A  342 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8279 (mtp-110)
REVERT: A  402 ARG cc_start: 0.7776 (mtt-85) cc_final: 0.7258 (mtp180)
REVERT: A  455 ARG cc_start: 0.7552 (mtm-85) cc_final: 0.7251 (mtt-85)
REVERT: A  504 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8443 (mp)
REVERT: A  523 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7287 (ttmm)
REVERT: A  583 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7789 (mtt90)
REVERT: E   84 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7435 (mp0)
REVERT: E  100 GLN cc_start: 0.8310 (mt0) cc_final: 0.8045 (mt0)
REVERT: E  200 LYS cc_start: 0.7158 (tptp) cc_final: 0.6673 (ttmt)
REVERT: E  233 THR cc_start: 0.7628 (p) cc_final: 0.7368 (t)
REVERT: E  267 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.7085 (p90)
REVERT: E  341 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7687 (mm-40)
REVERT: E  342 ARG cc_start: 0.8582 (mtp180) cc_final: 0.8243 (mtp-110)
REVERT: E  402 ARG cc_start: 0.7742 (mtt-85) cc_final: 0.7231 (mtp85)
REVERT: E  455 ARG cc_start: 0.7538 (mtm-85) cc_final: 0.7222 (mtt-85)
REVERT: E  504 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8443 (mp)
REVERT: E  523 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7288 (ttmm)
REVERT: E  583 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7796 (mtt90)
  outliers start: 55
  outliers final: 19
  residues processed: 147
  average time/residue: 0.5818
  time to fit residues: 91.8641
Evaluate side-chains
  134 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   29 ILE
Chi-restraints excluded: chain A residue   84 GLU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  267 HIS
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  480 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  523 LYS
Chi-restraints excluded: chain A residue  548 TRP
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain E residue   19 TYR
Chi-restraints excluded: chain E residue   84 GLU
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  267 HIS
Chi-restraints excluded: chain E residue  283 LEU
Chi-restraints excluded: chain E residue  341 GLN
Chi-restraints excluded: chain E residue  396 VAL
Chi-restraints excluded: chain E residue  398 VAL
Chi-restraints excluded: chain E residue  431 ASP
Chi-restraints excluded: chain E residue  480 VAL
Chi-restraints excluded: chain E residue  491 LEU
Chi-restraints excluded: chain E residue  504 ILE
Chi-restraints excluded: chain E residue  523 LYS
Chi-restraints excluded: chain E residue  548 TRP
Chi-restraints excluded: chain E residue  583 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0060
   chunk 111 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 52 optimal weight:    0.3980
   chunk 74 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 112 optimal weight:    0.6980
   chunk 80 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0050
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.3210

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN
E 271 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.165828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.131967 restraints weight = 12080.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.64
r_work: 0.3456 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10466  Z= 0.126
  Angle     :  0.580   9.100  14096  Z= 0.278
  Chirality :  0.041   0.289   1448
  Planarity :  0.004   0.043   1710
  Dihedral  : 14.347  72.734   1706
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 27.22 %
    Favored  : 68.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.26), residues: 1128
  helix:  2.75 (0.17), residues: 848
  sheet:  None (None), residues: 0
  loop : -2.83 (0.31), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 199 
 TYR   0.011   0.001   TYR A 450 
 PHE   0.017   0.001   PHE E 275 
 TRP   0.008   0.001   TRP E 542 
 HIS   0.002   0.000   HIS E 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (10464)
  covalent geometry    : angle       0.57952 (14092)
  SS BOND              : bond        0.00425 (    2)
  SS BOND              : angle       1.40751 (    4)
  hydrogen bonds       : bond        0.05471 (  668)
  hydrogen bonds       : angle       3.57187 ( 1992)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 114
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A   84 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7535 (mp0)
REVERT: A  100 GLN cc_start: 0.8315 (mt0) cc_final: 0.7978 (mt0)
REVERT: A  219 ASP cc_start: 0.7649 (m-30) cc_final: 0.7384 (t0)
REVERT: A  267 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.7315 (p-80)
REVERT: A  342 ARG cc_start: 0.8560 (mtp180) cc_final: 0.8288 (mtp-110)
REVERT: A  402 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7077 (mtp85)
REVERT: A  403 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7151 (ttp)
REVERT: A  455 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7191 (mtt-85)
REVERT: A  504 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8420 (mp)
REVERT: A  634 ARG cc_start: 0.7418 (ttt90) cc_final: 0.7114 (tpp80)
REVERT: E   84 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7545 (mp0)
REVERT: E  100 GLN cc_start: 0.8291 (mt0) cc_final: 0.7961 (mt0)
REVERT: E  219 ASP cc_start: 0.7629 (m-30) cc_final: 0.7378 (t0)
REVERT: E  267 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.7305 (p-80)
REVERT: E  341 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7610 (mm-40)
REVERT: E  342 ARG cc_start: 0.8575 (mtp180) cc_final: 0.8277 (mtp-110)
REVERT: E  402 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7061 (mtp85)
REVERT: E  403 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7149 (ttp)
REVERT: E  455 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7192 (mtt-85)
REVERT: E  504 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8419 (mp)
REVERT: E  634 ARG cc_start: 0.7411 (ttt90) cc_final: 0.7109 (tpp80)
  outliers start: 48
  outliers final: 8
  residues processed: 144
  average time/residue: 0.6007
  time to fit residues: 92.7591
Evaluate side-chains
  117 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 GLU
Chi-restraints excluded: chain A residue  103 ILE
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  267 HIS
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  455 ARG
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  548 TRP
Chi-restraints excluded: chain E residue   84 GLU
Chi-restraints excluded: chain E residue  103 ILE
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  267 HIS
Chi-restraints excluded: chain E residue  341 GLN
Chi-restraints excluded: chain E residue  402 ARG
Chi-restraints excluded: chain E residue  403 MET
Chi-restraints excluded: chain E residue  455 ARG
Chi-restraints excluded: chain E residue  491 LEU
Chi-restraints excluded: chain E residue  504 ILE
Chi-restraints excluded: chain E residue  548 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 106 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.159603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.124533 restraints weight = 11956.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.66
r_work: 0.3354 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10466  Z= 0.171
  Angle     :  0.613   9.417  14096  Z= 0.306
  Chirality :  0.043   0.245   1448
  Planarity :  0.004   0.046   1710
  Dihedral  : 14.390  77.590   1692
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 26.74 %
    Favored  : 67.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.25), residues: 1128
  helix:  2.58 (0.17), residues: 844
  sheet:  None (None), residues: 0
  loop : -2.79 (0.32), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 452 
 TYR   0.012   0.002   TYR A 528 
 PHE   0.023   0.002   PHE A 275 
 TRP   0.009   0.001   TRP A 217 
 HIS   0.004   0.001   HIS E 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (10464)
  covalent geometry    : angle       0.61247 (14092)
  SS BOND              : bond        0.00655 (    2)
  SS BOND              : angle       1.81653 (    4)
  hydrogen bonds       : bond        0.07308 (  668)
  hydrogen bonds       : angle       3.80237 ( 1992)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 104
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A   84 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7466 (mp0)
REVERT: A  100 GLN cc_start: 0.8355 (mt0) cc_final: 0.8017 (mt0)
REVERT: A  200 LYS cc_start: 0.7086 (tptp) cc_final: 0.6470 (mtmt)
REVERT: A  219 ASP cc_start: 0.7707 (m-30) cc_final: 0.7451 (t0)
REVERT: A  341 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7693 (mm-40)
REVERT: A  342 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8251 (mtp-110)
REVERT: A  402 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7223 (mtp180)
REVERT: A  455 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7222 (mtt-85)
REVERT: A  504 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8456 (mp)
REVERT: A  523 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7418 (ttmm)
REVERT: E   84 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7472 (mp0)
REVERT: E  100 GLN cc_start: 0.8358 (mt0) cc_final: 0.8023 (mt0)
REVERT: E  200 LYS cc_start: 0.6955 (tptp) cc_final: 0.6419 (mtmt)
REVERT: E  219 ASP cc_start: 0.7709 (m-30) cc_final: 0.7453 (t0)
REVERT: E  267 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.7243 (p-80)
REVERT: E  341 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7705 (mm-40)
REVERT: E  342 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8253 (mtp-110)
REVERT: E  402 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7277 (mtp85)
REVERT: E  455 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7217 (mtt-85)
REVERT: E  504 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8460 (mp)
REVERT: E  523 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7420 (ttmm)
REVERT: E  583 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7789 (mtt90)
  outliers start: 60
  outliers final: 18
  residues processed: 147
  average time/residue: 0.6040
  time to fit residues: 95.2330
Evaluate side-chains
  130 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 96
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   84 GLU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  455 ARG
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  523 LYS
Chi-restraints excluded: chain A residue  548 TRP
Chi-restraints excluded: chain E residue   19 TYR
Chi-restraints excluded: chain E residue   84 GLU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  173 LEU
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  267 HIS
Chi-restraints excluded: chain E residue  341 GLN
Chi-restraints excluded: chain E residue  342 ARG
Chi-restraints excluded: chain E residue  396 VAL
Chi-restraints excluded: chain E residue  398 VAL
Chi-restraints excluded: chain E residue  402 ARG
Chi-restraints excluded: chain E residue  431 ASP
Chi-restraints excluded: chain E residue  455 ARG
Chi-restraints excluded: chain E residue  491 LEU
Chi-restraints excluded: chain E residue  504 ILE
Chi-restraints excluded: chain E residue  523 LYS
Chi-restraints excluded: chain E residue  548 TRP
Chi-restraints excluded: chain E residue  583 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.161487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.126920 restraints weight = 12021.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.66
r_work: 0.3380 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10466  Z= 0.151
  Angle     :  0.601   9.546  14096  Z= 0.296
  Chirality :  0.042   0.224   1448
  Planarity :  0.004   0.044   1710
  Dihedral  : 13.984  86.747   1692
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 27.80 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.25), residues: 1128
  helix:  2.62 (0.17), residues: 844
  sheet:  None (None), residues: 0
  loop : -2.66 (0.32), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 199 
 TYR   0.012   0.002   TYR A 528 
 PHE   0.020   0.001   PHE A 275 
 TRP   0.008   0.001   TRP E 347 
 HIS   0.004   0.001   HIS A 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (10464)
  covalent geometry    : angle       0.60052 (14092)
  SS BOND              : bond        0.00595 (    2)
  SS BOND              : angle       1.71272 (    4)
  hydrogen bonds       : bond        0.06734 (  668)
  hydrogen bonds       : angle       3.73281 ( 1992)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 93
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   84 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7463 (mp0)
REVERT: A  100 GLN cc_start: 0.8345 (mt0) cc_final: 0.8002 (mt0)
REVERT: A  199 ARG cc_start: 0.6615 (tmm160) cc_final: 0.6363 (tmm160)
REVERT: A  200 LYS cc_start: 0.7056 (tptp) cc_final: 0.6474 (ttmt)
REVERT: A  219 ASP cc_start: 0.7681 (m-30) cc_final: 0.7438 (t0)
REVERT: A  341 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7701 (mm-40)
REVERT: A  342 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8265 (mtp180)
REVERT: A  402 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7181 (mtp85)
REVERT: A  455 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7182 (mtt-85)
REVERT: A  504 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8464 (mp)
REVERT: A  523 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7301 (ttmm)
REVERT: E   84 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7468 (mp0)
REVERT: E  100 GLN cc_start: 0.8328 (mt0) cc_final: 0.7987 (mt0)
REVERT: E  199 ARG cc_start: 0.6636 (tmm160) cc_final: 0.6383 (tmm160)
REVERT: E  200 LYS cc_start: 0.7044 (tptp) cc_final: 0.6496 (ttmt)
REVERT: E  219 ASP cc_start: 0.7686 (m-30) cc_final: 0.7441 (t0)
REVERT: E  341 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7732 (mm-40)
REVERT: E  342 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8253 (mtp-110)
REVERT: E  402 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7172 (mtp85)
REVERT: E  455 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7184 (mtt-85)
REVERT: E  504 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8469 (mp)
REVERT: E  523 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7305 (ttmm)
REVERT: E  583 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7774 (mtt90)
REVERT: E  612 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7046 (mpp)
  outliers start: 50
  outliers final: 18
  residues processed: 128
  average time/residue: 0.5791
  time to fit residues: 79.6361
Evaluate side-chains
  125 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 91
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 TYR
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   84 GLU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  455 ARG
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  523 LYS
Chi-restraints excluded: chain A residue  548 TRP
Chi-restraints excluded: chain E residue   19 TYR
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue   84 GLU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  341 GLN
Chi-restraints excluded: chain E residue  342 ARG
Chi-restraints excluded: chain E residue  396 VAL
Chi-restraints excluded: chain E residue  402 ARG
Chi-restraints excluded: chain E residue  431 ASP
Chi-restraints excluded: chain E residue  455 ARG
Chi-restraints excluded: chain E residue  463 SER
Chi-restraints excluded: chain E residue  491 LEU
Chi-restraints excluded: chain E residue  504 ILE
Chi-restraints excluded: chain E residue  523 LYS
Chi-restraints excluded: chain E residue  548 TRP
Chi-restraints excluded: chain E residue  583 ARG
Chi-restraints excluded: chain E residue  612 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0980
   chunk 21 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 102 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  74 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.162059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.127544 restraints weight = 11799.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.64
r_work: 0.3385 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10466  Z= 0.143
  Angle     :  0.578   9.906  14096  Z= 0.288
  Chirality :  0.041   0.204   1448
  Planarity :  0.004   0.043   1710
  Dihedral  : 13.335  82.649   1692
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 28.19 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.25), residues: 1128
  helix:  2.69 (0.17), residues: 846
  sheet:  None (None), residues: 0
  loop : -2.74 (0.32), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 199 
 TYR   0.011   0.001   TYR A 528 
 PHE   0.021   0.001   PHE E 275 
 TRP   0.007   0.001   TRP A 217 
 HIS   0.004   0.001   HIS E 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10464)
  covalent geometry    : angle       0.57697 (14092)
  SS BOND              : bond        0.00582 (    2)
  SS BOND              : angle       1.62810 (    4)
  hydrogen bonds       : bond        0.06501 (  668)
  hydrogen bonds       : angle       3.68520 ( 1992)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 97
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A   84 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7479 (mp0)
REVERT: A  100 GLN cc_start: 0.8254 (mt0) cc_final: 0.7943 (mt0)
REVERT: A  200 LYS cc_start: 0.7093 (tptp) cc_final: 0.6518 (mtmt)
REVERT: A  219 ASP cc_start: 0.7669 (m-30) cc_final: 0.7439 (t0)
REVERT: A  341 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7733 (mm-40)
REVERT: A  342 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8218 (mtp180)
REVERT: A  402 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7160 (mtp85)
REVERT: A  455 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7150 (mtt-85)
REVERT: A  504 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8442 (mp)
REVERT: A  523 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7270 (ttmm)
REVERT: E   84 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7497 (mp0)
REVERT: E  100 GLN cc_start: 0.8297 (mt0) cc_final: 0.7947 (mt0)
REVERT: E  200 LYS cc_start: 0.7085 (tptp) cc_final: 0.6508 (mtmt)
REVERT: E  219 ASP cc_start: 0.7676 (m-30) cc_final: 0.7442 (t0)
REVERT: E  341 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7695 (mm-40)
REVERT: E  342 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8222 (mtp-110)
REVERT: E  402 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7156 (mtp85)
REVERT: E  455 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7155 (mtt-85)
REVERT: E  504 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8443 (mp)
REVERT: E  523 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7270 (ttmm)
REVERT: E  583 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7712 (mtt90)
REVERT: E  612 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7031 (mpp)
  outliers start: 47
  outliers final: 13
  residues processed: 128
  average time/residue: 0.6038
  time to fit residues: 82.9802
Evaluate side-chains
  121 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   84 GLU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  455 ARG
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  523 LYS
Chi-restraints excluded: chain A residue  548 TRP
Chi-restraints excluded: chain E residue   84 GLU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  341 GLN
Chi-restraints excluded: chain E residue  342 ARG
Chi-restraints excluded: chain E residue  396 VAL
Chi-restraints excluded: chain E residue  402 ARG
Chi-restraints excluded: chain E residue  431 ASP
Chi-restraints excluded: chain E residue  455 ARG
Chi-restraints excluded: chain E residue  491 LEU
Chi-restraints excluded: chain E residue  504 ILE
Chi-restraints excluded: chain E residue  523 LYS
Chi-restraints excluded: chain E residue  548 TRP
Chi-restraints excluded: chain E residue  583 ARG
Chi-restraints excluded: chain E residue  612 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
E  74 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.160442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.125907 restraints weight = 11857.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 1.64
r_work: 0.3365 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10466  Z= 0.157
  Angle     :  0.590  10.013  14096  Z= 0.296
  Chirality :  0.041   0.192   1448
  Planarity :  0.004   0.044   1710
  Dihedral  : 13.042  74.596   1692
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 28.38 %
    Favored  : 67.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.25), residues: 1128
  helix:  2.60 (0.17), residues: 844
  sheet:  None (None), residues: 0
  loop : -2.58 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 199 
 TYR   0.011   0.002   TYR A 528 
 PHE   0.022   0.001   PHE E 275 
 TRP   0.009   0.001   TRP E 217 
 HIS   0.004   0.001   HIS E 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10464)
  covalent geometry    : angle       0.58950 (14092)
  SS BOND              : bond        0.00634 (    2)
  SS BOND              : angle       1.77516 (    4)
  hydrogen bonds       : bond        0.07046 (  668)
  hydrogen bonds       : angle       3.75182 ( 1992)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 91
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A   84 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7478 (mp0)
REVERT: A  100 GLN cc_start: 0.8325 (mt0) cc_final: 0.8013 (mt0)
REVERT: A  200 LYS cc_start: 0.7177 (tptp) cc_final: 0.6550 (mtmt)
REVERT: A  219 ASP cc_start: 0.7669 (m-30) cc_final: 0.7450 (t0)
REVERT: A  341 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7758 (mm-40)
REVERT: A  342 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8203 (mtp180)
REVERT: A  402 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7272 (mtp180)
REVERT: A  455 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7182 (mtt-85)
REVERT: A  504 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8463 (mp)
REVERT: A  523 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7376 (ttmm)
REVERT: E   84 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7482 (mp0)
REVERT: E  100 GLN cc_start: 0.8317 (mt0) cc_final: 0.8001 (mt0)
REVERT: E  200 LYS cc_start: 0.7116 (tptp) cc_final: 0.6532 (mtmt)
REVERT: E  219 ASP cc_start: 0.7652 (m-30) cc_final: 0.7447 (t0)
REVERT: E  341 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7770 (mm-40)
REVERT: E  342 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8216 (mtp-110)
REVERT: E  402 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7256 (mtp85)
REVERT: E  455 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7179 (mtt-85)
REVERT: E  504 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8467 (mp)
REVERT: E  523 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7385 (ttmm)
REVERT: E  583 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7793 (mtt90)
REVERT: E  612 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7110 (mpp)
  outliers start: 47
  outliers final: 20
  residues processed: 127
  average time/residue: 0.5552
  time to fit residues: 75.8396
Evaluate side-chains
  125 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 89
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   84 GLU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  455 ARG
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  480 VAL
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  523 LYS
Chi-restraints excluded: chain A residue  548 TRP
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue   84 GLU
Chi-restraints excluded: chain E residue  173 LEU
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  341 GLN
Chi-restraints excluded: chain E residue  342 ARG
Chi-restraints excluded: chain E residue  396 VAL
Chi-restraints excluded: chain E residue  402 ARG
Chi-restraints excluded: chain E residue  431 ASP
Chi-restraints excluded: chain E residue  455 ARG
Chi-restraints excluded: chain E residue  463 SER
Chi-restraints excluded: chain E residue  480 VAL
Chi-restraints excluded: chain E residue  491 LEU
Chi-restraints excluded: chain E residue  504 ILE
Chi-restraints excluded: chain E residue  523 LYS
Chi-restraints excluded: chain E residue  548 TRP
Chi-restraints excluded: chain E residue  583 ARG
Chi-restraints excluded: chain E residue  612 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0470
   chunk 20 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6280

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.160596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.126094 restraints weight = 11808.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.61
r_work: 0.3378 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10466  Z= 0.148
  Angle     :  0.577  10.089  14096  Z= 0.290
  Chirality :  0.041   0.196   1448
  Planarity :  0.004   0.043   1710
  Dihedral  : 12.583  71.611   1692
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 29.34 %
    Favored  : 67.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.25), residues: 1128
  helix:  2.66 (0.17), residues: 844
  sheet:  None (None), residues: 0
  loop : -2.56 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 199 
 TYR   0.012   0.001   TYR A 224 
 PHE   0.021   0.001   PHE A 275 
 TRP   0.008   0.001   TRP A 217 
 HIS   0.004   0.001   HIS E 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (10464)
  covalent geometry    : angle       0.57633 (14092)
  SS BOND              : bond        0.00586 (    2)
  SS BOND              : angle       1.66130 (    4)
  hydrogen bonds       : bond        0.06706 (  668)
  hydrogen bonds       : angle       3.70777 ( 1992)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 99
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A   84 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7503 (mp0)
REVERT: A  100 GLN cc_start: 0.8313 (mt0) cc_final: 0.7960 (mt0)
REVERT: A  200 LYS cc_start: 0.7149 (tptp) cc_final: 0.6582 (mtmt)
REVERT: A  219 ASP cc_start: 0.7665 (m-30) cc_final: 0.7458 (t0)
REVERT: A  341 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7749 (mm-40)
REVERT: A  342 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8213 (mtp180)
REVERT: A  402 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7254 (mtp180)
REVERT: A  455 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7181 (mtt-85)
REVERT: A  504 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8485 (mp)
REVERT: A  523 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7313 (ttmm)
REVERT: E   84 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7511 (mp0)
REVERT: E  100 GLN cc_start: 0.8263 (mt0) cc_final: 0.7953 (mt0)
REVERT: E  200 LYS cc_start: 0.7124 (tptp) cc_final: 0.6559 (mtmt)
REVERT: E  219 ASP cc_start: 0.7676 (m-30) cc_final: 0.7466 (t0)
REVERT: E  341 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7740 (mm-40)
REVERT: E  342 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8224 (mtp-110)
REVERT: E  402 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7243 (mtp180)
REVERT: E  455 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7180 (mtt-85)
REVERT: E  504 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8488 (mp)
REVERT: E  523 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7322 (ttmm)
REVERT: E  583 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7738 (mtt90)
REVERT: E  612 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7057 (mpp)
  outliers start: 36
  outliers final: 18
  residues processed: 125
  average time/residue: 0.5677
  time to fit residues: 76.4536
Evaluate side-chains
  131 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 97
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   84 GLU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  455 ARG
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  523 LYS
Chi-restraints excluded: chain A residue  548 TRP
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue   84 GLU
Chi-restraints excluded: chain E residue  173 LEU
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  341 GLN
Chi-restraints excluded: chain E residue  342 ARG
Chi-restraints excluded: chain E residue  402 ARG
Chi-restraints excluded: chain E residue  431 ASP
Chi-restraints excluded: chain E residue  455 ARG
Chi-restraints excluded: chain E residue  463 SER
Chi-restraints excluded: chain E residue  491 LEU
Chi-restraints excluded: chain E residue  504 ILE
Chi-restraints excluded: chain E residue  523 LYS
Chi-restraints excluded: chain E residue  548 TRP
Chi-restraints excluded: chain E residue  583 ARG
Chi-restraints excluded: chain E residue  612 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 106 optimal weight:    0.0000
   chunk 58 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 104 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.5384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.161699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.127282 restraints weight = 11728.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 1.61
r_work: 0.3394 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10466  Z= 0.141
  Angle     :  0.588  10.316  14096  Z= 0.291
  Chirality :  0.040   0.207   1448
  Planarity :  0.004   0.043   1710
  Dihedral  : 12.248  72.058   1692
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 29.44 %
    Favored  : 66.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.24 (0.25), residues: 1128
  helix:  2.69 (0.17), residues: 846
  sheet:  None (None), residues: 0
  loop : -2.60 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 199 
 TYR   0.012   0.001   TYR E 224 
 PHE   0.020   0.001   PHE E 275 
 TRP   0.007   0.001   TRP E 570 
 HIS   0.003   0.001   HIS A 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10464)
  covalent geometry    : angle       0.58701 (14092)
  SS BOND              : bond        0.00545 (    2)
  SS BOND              : angle       1.60668 (    4)
  hydrogen bonds       : bond        0.06441 (  668)
  hydrogen bonds       : angle       3.67121 ( 1992)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 97
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A   84 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7508 (mp0)
REVERT: A  100 GLN cc_start: 0.8333 (mt0) cc_final: 0.7994 (mt0)
REVERT: A  200 LYS cc_start: 0.7003 (tptp) cc_final: 0.6485 (mtmt)
REVERT: A  341 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7749 (mm-40)
REVERT: A  342 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8229 (mtp180)
REVERT: A  402 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7360 (mtp180)
REVERT: A  455 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7248 (mtt-85)
REVERT: A  504 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8497 (mp)
REVERT: A  523 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7262 (ttmm)
REVERT: E   84 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7558 (mp0)
REVERT: E  100 GLN cc_start: 0.8327 (mt0) cc_final: 0.8015 (mt0)
REVERT: E  200 LYS cc_start: 0.6993 (tptp) cc_final: 0.6473 (mtmt)
REVERT: E  341 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7745 (mm-40)
REVERT: E  342 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8249 (mtp-110)
REVERT: E  402 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7333 (mtp180)
REVERT: E  455 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7259 (mtt-85)
REVERT: E  504 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8500 (mp)
REVERT: E  523 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7270 (ttmm)
REVERT: E  583 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7780 (mtt90)
  outliers start: 37
  outliers final: 17
  residues processed: 123
  average time/residue: 0.5853
  time to fit residues: 77.5505
Evaluate side-chains
  124 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 92
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   84 GLU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  342 ARG
Chi-restraints excluded: chain A residue  402 ARG
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  455 ARG
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  491 LEU
Chi-restraints excluded: chain A residue  504 ILE
Chi-restraints excluded: chain A residue  523 LYS
Chi-restraints excluded: chain A residue  548 TRP
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue   84 GLU
Chi-restraints excluded: chain E residue  173 LEU
Chi-restraints excluded: chain E residue  341 GLN
Chi-restraints excluded: chain E residue  342 ARG
Chi-restraints excluded: chain E residue  402 ARG
Chi-restraints excluded: chain E residue  431 ASP
Chi-restraints excluded: chain E residue  455 ARG
Chi-restraints excluded: chain E residue  463 SER
Chi-restraints excluded: chain E residue  491 LEU
Chi-restraints excluded: chain E residue  504 ILE
Chi-restraints excluded: chain E residue  523 LYS
Chi-restraints excluded: chain E residue  548 TRP
Chi-restraints excluded: chain E residue  583 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 90 optimal weight:    0.5980
   chunk 65 optimal weight:    9.9990
   chunk 80 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.160987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.126555 restraints weight = 11931.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.64
r_work: 0.3372 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10466  Z= 0.158
  Angle     :  0.600  10.195  14096  Z= 0.303
  Chirality :  0.041   0.208   1448
  Planarity :  0.004   0.054   1710
  Dihedral  : 12.290  76.735   1692
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 29.44 %
    Favored  : 66.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.25), residues: 1128
  helix:  2.61 (0.17), residues: 844
  sheet:  None (None), residues: 0
  loop : -2.52 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG E 199 
 TYR   0.014   0.002   TYR A 224 
 PHE   0.022   0.001   PHE E 275 
 TRP   0.009   0.001   TRP A 217 
 HIS   0.004   0.001   HIS A 598 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (10464)
  covalent geometry    : angle       0.59903 (14092)
  SS BOND              : bond        0.00613 (    2)
  SS BOND              : angle       1.69077 (    4)
  hydrogen bonds       : bond        0.06995 (  668)
  hydrogen bonds       : angle       3.74797 ( 1992)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3410.18 seconds
wall clock time: 58 minutes 45.39 seconds (3525.39 seconds total)