Starting phenix.real_space_refine
on Sat Apr  4 22:44:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9t3r_55517/04_2026/9t3r_55517.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9t3r_55517/04_2026/9t3r_55517.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9t3r_55517/04_2026/9t3r_55517.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9t3r_55517/04_2026/9t3r_55517.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9t3r_55517/04_2026/9t3r_55517.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9t3r_55517/04_2026/9t3r_55517.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    3177      2.51       5
     N     890      2.21       5
     O     973      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  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: 5077
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "L"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 783
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 906
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 2, 'TRANS': 115}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 437, 3388
          Classifications: {'peptide': 437}
          Link IDs: {'PTRANS': 23, 'TRANS': 413}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.23, per 1000 atoms: 0.24
  Number of scatterers: 5077
  At special positions: 0
  Unit cell: (100.602, 102.789, 72.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O     973      8.00
     N     890      7.00
     C    3177      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  26 " - pdb=" SG  CYS A  53 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 199 " - pdb=" SG  CYS A 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 227 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 224 " - pdb=" SG  CYS A 235 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 236 " - pdb=" SG  CYS A 244 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 252 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 255 " - pdb=" SG  CYS A 264 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 268 " - pdb=" SG  CYS A 295 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 299 " - pdb=" SG  CYS A 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 342 " - pdb=" SG  CYS A 367 " distance=2.03

  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: 0.39
  Conformation dependent library (CDL) restraints added in 313.8 milliseconds
  

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1214

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 14 sheets defined
      11.0% alpha, 23.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 41
    Processing helix  chain 'A' and resid 42 through 50
    Processing helix  chain 'A' and resid 71 through 77
      removed outlier: 3.637A  pdb=" N   GLN A  75 " --> pdb=" O   SER A  72 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ASP A  76 " --> pdb=" O   PHE A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 3.856A  pdb=" N   ILE A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 212
      removed outlier: 4.235A  pdb=" N   CYS A 212 " --> pdb=" O   SER A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 279
      removed outlier: 4.148A  pdb=" N   PHE A 279 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 276 through 279'
    Processing helix  chain 'A' and resid 347 through 352
      removed outlier: 4.214A  pdb=" N   GLU A 352 " --> pdb=" O   HIS A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 365
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.680A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 401
    Processing helix  chain 'A' and resid 422 through 426
    Processing helix  chain 'A' and resid 436 through 439
    Processing helix  chain 'A' and resid 481 through 486
      removed outlier: 3.615A  pdb=" N   PHE A 486 " --> pdb=" O   TRP A 482 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.794A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 108 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   TRP L  37 " --> pdb=" O   MET L  49 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.794A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 108 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   SER L  98 " --> pdb=" O   THR L  94 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 5
      removed outlier: 3.945A  pdb=" N   ALA H  79 " --> pdb=" O   CYS H  22 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.679A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.679A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   TYR H 111 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 17 through 19
    Processing sheet with id=AA8, first strand: chain 'A' and resid 25 through 26
    Processing sheet with id=AA9, first strand: chain 'A' and resid 61 through 63
      removed outlier: 5.044A  pdb=" N   TYR A 112 " --> pdb=" O   GLY A 152 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   LEU A 154 " --> pdb=" O   TYR A 112 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   LEU A 114 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   GLN A 156 " --> pdb=" O   LEU A 114 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   VAL A 116 " --> pdb=" O   GLN A 156 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 258 through 260
    Processing sheet with id=AB2, first strand: chain 'A' and resid 272 through 274
    Processing sheet with id=AB3, first strand: chain 'A' and resid 289 through 291
    Processing sheet with id=AB4, first strand: chain 'A' and resid 369 through 370
    Processing sheet with id=AB5, first strand: chain 'A' and resid 374 through 376
      removed outlier: 6.449A  pdb=" N   LEU A 374 " --> pdb=" O   TYR A 411 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   LEU A 467 " --> pdb=" O   SER A 442 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   THR A 444 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   HIS A 469 " --> pdb=" O   THR A 444 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   GLN A 446 " --> pdb=" O   HIS A 469 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ALA A 466 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 8.315A  pdb=" N   THR A 496 " --> pdb=" O   ALA A 466 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ILE A 468 " --> pdb=" O   THR A 496 " (cutoff:3.500A)

    111 hydrogen bonds defined for protein.
    222 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: 0.74

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1688
        1.34 -     1.46: 1156
        1.46 -     1.58: 2297
        1.58 -     1.70: 0
        1.70 -     1.81: 45
  Bond restraints: 5186
  Sorted by residual:
  bond pdb=" C   LEU A 392 "
       pdb=" N   GLN A 393 "
    ideal  model  delta    sigma   weight residual
    1.331  1.295  0.036 2.83e-02 1.25e+03 1.61e+00
  bond pdb=" CB  ASP L  84 "
       pdb=" CG  ASP L  84 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.39e+00
  bond pdb=" CB  GLN H   6 "
       pdb=" CG  GLN H   6 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.50e-01
  bond pdb=" CA  ASP L  84 "
       pdb=" CB  ASP L  84 "
    ideal  model  delta    sigma   weight residual
    1.528  1.545 -0.017 1.82e-02 3.02e+03 9.01e-01
  bond pdb=" CB  GLN H 103 "
       pdb=" CG  GLN H 103 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 9.00e-01
  ... (remaining 5181 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 6892
        1.61 -     3.22: 133
        3.22 -     4.82: 18
        4.82 -     6.43: 4
        6.43 -     8.04: 1
  Bond angle restraints: 7048
  Sorted by residual:
  angle pdb=" CA  ASP L  84 "
        pdb=" CB  ASP L  84 "
        pdb=" CG  ASP L  84 "
      ideal   model   delta    sigma   weight residual
     112.60  115.64   -3.04 1.00e+00 1.00e+00 9.26e+00
  angle pdb=" C   SER A 387 "
        pdb=" N   ASN A 388 "
        pdb=" CA  ASN A 388 "
      ideal   model   delta    sigma   weight residual
     121.54  127.30   -5.76 1.91e+00 2.74e-01 9.09e+00
  angle pdb=" CB  GLN H   6 "
        pdb=" CG  GLN H   6 "
        pdb=" CD  GLN H   6 "
      ideal   model   delta    sigma   weight residual
     112.60  117.32   -4.72 1.70e+00 3.46e-01 7.72e+00
  angle pdb=" C   TYR A 301 "
        pdb=" N   ASN A 302 "
        pdb=" CA  ASN A 302 "
      ideal   model   delta    sigma   weight residual
     122.61  126.84   -4.23 1.56e+00 4.11e-01 7.34e+00
  angle pdb=" CA  GLN H   6 "
        pdb=" CB  GLN H   6 "
        pdb=" CG  GLN H   6 "
      ideal   model   delta    sigma   weight residual
     114.10  119.34   -5.24 2.00e+00 2.50e-01 6.85e+00
  ... (remaining 7043 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2674
       17.95 -    35.91: 340
       35.91 -    53.86: 78
       53.86 -    71.81: 14
       71.81 -    89.76: 7
  Dihedral angle restraints: 3113
    sinusoidal: 1216
      harmonic: 1897
  Sorted by residual:
  dihedral pdb=" CA  CYS A 255 "
           pdb=" C   CYS A 255 "
           pdb=" N   LEU A 256 "
           pdb=" CA  LEU A 256 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.89  -25.11     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CB  CYS A 224 "
           pdb=" SG  CYS A 224 "
           pdb=" SG  CYS A 235 "
           pdb=" CB  CYS A 235 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.18   39.18     1      1.00e+01 1.00e-02 2.16e+01
  dihedral pdb=" CB  CYS A 220 "
           pdb=" SG  CYS A 220 "
           pdb=" SG  CYS A 227 "
           pdb=" CB  CYS A 227 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -123.97   37.97     1      1.00e+01 1.00e-02 2.03e+01
  ... (remaining 3110 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 463
       0.030 -    0.059: 228
       0.059 -    0.089: 45
       0.089 -    0.119: 49
       0.119 -    0.148: 11
  Chirality restraints: 796
  Sorted by residual:
  chirality pdb=" CA  ASN A 302 "
            pdb=" N   ASN A 302 "
            pdb=" C   ASN A 302 "
            pdb=" CB  ASN A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  ASN A 388 "
            pdb=" N   ASN A 388 "
            pdb=" C   ASN A 388 "
            pdb=" CB  ASN A 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CA  ILE A 263 "
            pdb=" N   ILE A 263 "
            pdb=" C   ILE A 263 "
            pdb=" CB  ILE A 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  ... (remaining 793 not shown)

  Planarity restraints: 911
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP L  84 "   -0.017 2.00e-02 2.50e+03   3.37e-02 1.13e+01
        pdb=" C   ASP L  84 "    0.058 2.00e-02 2.50e+03
        pdb=" O   ASP L  84 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLU L  85 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A  30 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   ASP A  30 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ASP A  30 "    0.011 2.00e-02 2.50e+03
        pdb=" N   MET A  31 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  64 "   -0.004 2.00e-02 2.50e+03   8.93e-03 1.60e+00
        pdb=" CG  TYR A  64 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  64 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  64 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  64 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  64 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  64 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A  64 "    0.001 2.00e-02 2.50e+03
  ... (remaining 908 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1812
        2.86 -     3.37: 4458
        3.37 -     3.88: 8139
        3.88 -     4.39: 9536
        4.39 -     4.90: 16196
  Nonbonded interactions: 40141
  Sorted by model distance:
  nonbonded pdb=" O   ASP L  84 "
            pdb=" OD1 ASP L  84 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   ASP A  30 "
            pdb=" OD1 ASP A  30 "
     model   vdw
     2.428 3.040
  nonbonded pdb=" O   TYR A 301 "
            pdb=" OD1 ASN A 302 "
     model   vdw
     2.488 3.040
  nonbonded pdb=" O   SER A 387 "
            pdb=" OD1 ASN A 388 "
     model   vdw
     2.524 3.040
  nonbonded pdb=" N   GLN H   6 "
            pdb=" OE1 GLN H   6 "
     model   vdw
     2.546 3.120
  ... (remaining 40136 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.180
  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:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.620
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
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      :  0.003   0.036   5200  Z= 0.143
  Angle     :  0.574   8.039   7076  Z= 0.315
  Chirality :  0.043   0.148    796
  Planarity :  0.004   0.034    911
  Dihedral  : 16.729  89.764   1857
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 23.98 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.34), residues: 651
  helix: -4.27 (0.53), residues: 22
  sheet: -1.40 (0.39), residues: 177
  loop : -0.63 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  98 
 TYR   0.020   0.001   TYR A  64 
 PHE   0.007   0.001   PHE A 400 
 TRP   0.015   0.001   TRP H  36 
 HIS   0.002   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5186)
  covalent geometry    : angle       0.57253 ( 7048)
  SS BOND              : bond        0.00226 (   14)
  SS BOND              : angle       0.83461 (   28)
  hydrogen bonds       : bond        0.23334 (  105)
  hydrogen bonds       : angle      10.08568 (  222)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.189 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.6471 (tt0) cc_final: 0.5922 (mt-10)
REVERT: H   65 GLN cc_start: 0.7390 (tp-100) cc_final: 0.7164 (tp-100)
REVERT: A  190 ARG cc_start: 0.6765 (ptt180) cc_final: 0.5715 (ptt90)
REVERT: A  450 ILE cc_start: 0.7410 (mm) cc_final: 0.6589 (pt)
  outliers start: 22
  outliers final: 19
  residues processed: 85
  average time/residue: 0.0612
  time to fit residues: 7.1403
Evaluate side-chains
  87 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue  108 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   75 SER
Chi-restraints excluded: chain H residue   81 MET
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain A residue   26 CYS
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  164 GLN
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  255 CYS
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  457 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    0.0470
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0980
   chunk 33 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.2980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    0.3078

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

Flipped N/Q/H residues before XYZ refinement:
L  41 HIS
L  62 ASN
A  42 HIS
A  59 ASN
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 ASN
A 470 HIS
A 491 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.142049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.119958 restraints weight = 6942.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.124044 restraints weight = 4184.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.127002 restraints weight = 2906.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.129049 restraints weight = 2194.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.130536 restraints weight = 1766.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.0841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5200  Z= 0.101
  Angle     :  0.496   5.850   7076  Z= 0.267
  Chirality :  0.042   0.139    796
  Planarity :  0.003   0.026    911
  Dihedral  :  5.575  41.819    739
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.38 %
    Favored  : 74.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.34), residues: 651
  helix: -3.75 (0.79), residues: 23
  sheet: -1.28 (0.39), residues: 179
  loop : -0.53 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  98 
 TYR   0.015   0.001   TYR A  64 
 PHE   0.013   0.001   PHE A  73 
 TRP   0.007   0.001   TRP A 205 
 HIS   0.002   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 5186)
  covalent geometry    : angle       0.49365 ( 7048)
  SS BOND              : bond        0.00299 (   14)
  SS BOND              : angle       0.91679 (   28)
  hydrogen bonds       : bond        0.03445 (  105)
  hydrogen bonds       : angle       6.62146 (  222)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.205 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.5864 (mt-10)
REVERT: H   81 MET cc_start: 0.8449 (ttm) cc_final: 0.8237 (ttm)
REVERT: A  399 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7808 (t)
REVERT: A  450 ILE cc_start: 0.7320 (mm) cc_final: 0.6506 (pt)
  outliers start: 19
  outliers final: 6
  residues processed: 87
  average time/residue: 0.0640
  time to fit residues: 7.5990
Evaluate side-chains
  78 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  108 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  237 HIS
Chi-restraints excluded: chain A residue  302 ASN
Chi-restraints excluded: chain A residue  399 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0870
   chunk 27 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.8164

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

Flipped N/Q/H residues before XYZ refinement:
L  62 ASN
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.138666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.116542 restraints weight = 6965.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.120646 restraints weight = 4192.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.123561 restraints weight = 2911.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.125503 restraints weight = 2199.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.127076 restraints weight = 1789.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.1077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5200  Z= 0.164
  Angle     :  0.546   8.471   7076  Z= 0.287
  Chirality :  0.044   0.150    796
  Planarity :  0.003   0.026    911
  Dihedral  :  4.616  29.425    716
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 21.31 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.35 (0.34), residues: 651
  helix: -3.77 (0.81), residues: 23
  sheet: -1.07 (0.39), residues: 172
  loop : -0.64 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 434 
 TYR   0.015   0.001   TYR H  95 
 PHE   0.009   0.001   PHE A  73 
 TRP   0.012   0.002   TRP A 205 
 HIS   0.002   0.001   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 5186)
  covalent geometry    : angle       0.54262 ( 7048)
  SS BOND              : bond        0.00371 (   14)
  SS BOND              : angle       1.08808 (   28)
  hydrogen bonds       : bond        0.03492 (  105)
  hydrogen bonds       : angle       6.34062 (  222)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 74
  time to evaluate  : 0.215 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.5929 (mt-10)
REVERT: A  188 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6928 (mmt90)
REVERT: A  399 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7782 (t)
REVERT: A  450 ILE cc_start: 0.7392 (mm) cc_final: 0.6467 (pt)
  outliers start: 29
  outliers final: 17
  residues processed: 93
  average time/residue: 0.0646
  time to fit residues: 8.1602
Evaluate side-chains
  90 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue   99 LEU
Chi-restraints excluded: chain L residue  108 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   34 MET
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   26 CYS
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  249 HIS
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  424 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 53 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** L  33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  55 ASN
L  62 ASN
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 275 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.136560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.114629 restraints weight = 7050.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.118707 restraints weight = 4255.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.121552 restraints weight = 2954.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.123597 restraints weight = 2240.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.125110 restraints weight = 1803.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5200  Z= 0.192
  Angle     :  0.574   7.447   7076  Z= 0.303
  Chirality :  0.045   0.144    796
  Planarity :  0.004   0.026    911
  Dihedral  :  4.881  30.289    716
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 20.43 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.43 (0.33), residues: 651
  helix: -3.77 (0.81), residues: 23
  sheet: -1.08 (0.39), residues: 172
  loop : -0.72 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 354 
 TYR   0.017   0.002   TYR A  64 
 PHE   0.008   0.002   PHE A 279 
 TRP   0.015   0.002   TRP A 205 
 HIS   0.003   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 5186)
  covalent geometry    : angle       0.57104 ( 7048)
  SS BOND              : bond        0.00447 (   14)
  SS BOND              : angle       1.15113 (   28)
  hydrogen bonds       : bond        0.03478 (  105)
  hydrogen bonds       : angle       6.26839 (  222)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 70
  time to evaluate  : 0.125 
Fit side-chains
REVERT: L   54 SER cc_start: 0.9043 (p) cc_final: 0.8716 (p)
REVERT: H   34 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7809 (mmp)
REVERT: H   46 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6053 (mt-10)
REVERT: A  188 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6882 (mmt90)
REVERT: A  399 VAL cc_start: 0.8029 (OUTLIER) cc_final: 0.7753 (t)
REVERT: A  450 ILE cc_start: 0.7348 (mm) cc_final: 0.6364 (pt)
  outliers start: 34
  outliers final: 20
  residues processed: 93
  average time/residue: 0.0810
  time to fit residues: 9.7605
Evaluate side-chains
  90 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   99 LEU
Chi-restraints excluded: chain L residue  108 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   34 MET
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain A residue   26 CYS
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  138 ARG
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  249 HIS
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0170
   chunk 3 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
L  62 ASN
A 158 ASN
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.138858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.116848 restraints weight = 7028.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.120937 restraints weight = 4195.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.123864 restraints weight = 2893.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.125853 restraints weight = 2177.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.127427 restraints weight = 1756.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5200  Z= 0.132
  Angle     :  0.533   6.554   7076  Z= 0.283
  Chirality :  0.043   0.142    796
  Planarity :  0.003   0.026    911
  Dihedral  :  4.611  30.232    716
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 20.25 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.34), residues: 651
  helix: -3.72 (0.82), residues: 23
  sheet: -1.00 (0.40), residues: 173
  loop : -0.70 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 434 
 TYR   0.015   0.001   TYR A  64 
 PHE   0.007   0.001   PHE A  73 
 TRP   0.011   0.001   TRP A 205 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 5186)
  covalent geometry    : angle       0.53069 ( 7048)
  SS BOND              : bond        0.00323 (   14)
  SS BOND              : angle       0.93819 (   28)
  hydrogen bonds       : bond        0.02990 (  105)
  hydrogen bonds       : angle       5.92012 (  222)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 71
  time to evaluate  : 0.190 
Fit side-chains
REVERT: L   54 SER cc_start: 0.8902 (p) cc_final: 0.8587 (p)
REVERT: H   46 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5964 (mt-10)
REVERT: A  188 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6837 (mmt90)
REVERT: A  399 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7759 (t)
REVERT: A  450 ILE cc_start: 0.7262 (mm) cc_final: 0.6299 (pt)
  outliers start: 30
  outliers final: 19
  residues processed: 89
  average time/residue: 0.0664
  time to fit residues: 7.9133
Evaluate side-chains
  90 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue  108 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain A residue   26 CYS
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  237 HIS
Chi-restraints excluded: chain A residue  249 HIS
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0870
   chunk 40 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 4 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9980
   chunk 54 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** L  33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  62 ASN
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.139204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.117164 restraints weight = 7055.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.121320 restraints weight = 4216.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.124236 restraints weight = 2900.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.126381 restraints weight = 2180.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.127966 restraints weight = 1736.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5200  Z= 0.130
  Angle     :  0.527   6.859   7076  Z= 0.278
  Chirality :  0.043   0.143    796
  Planarity :  0.003   0.026    911
  Dihedral  :  4.545  30.312    716
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 19.36 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.32 (0.34), residues: 651
  helix: -3.57 (0.85), residues: 23
  sheet: -0.96 (0.40), residues: 173
  loop : -0.67 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 354 
 TYR   0.013   0.001   TYR A 274 
 PHE   0.007   0.001   PHE A 364 
 TRP   0.011   0.001   TRP A 205 
 HIS   0.002   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 5186)
  covalent geometry    : angle       0.52461 ( 7048)
  SS BOND              : bond        0.00313 (   14)
  SS BOND              : angle       0.95968 (   28)
  hydrogen bonds       : bond        0.02978 (  105)
  hydrogen bonds       : angle       5.73294 (  222)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 72
  time to evaluate  : 0.198 
Fit side-chains
REVERT: L   54 SER cc_start: 0.8882 (p) cc_final: 0.8541 (p)
REVERT: H   34 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7716 (mmp)
REVERT: H   46 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.5945 (mt-10)
REVERT: A  188 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6818 (mmt90)
REVERT: A  399 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7726 (t)
REVERT: A  450 ILE cc_start: 0.7251 (mm) cc_final: 0.6292 (pt)
  outliers start: 33
  outliers final: 23
  residues processed: 93
  average time/residue: 0.0729
  time to fit residues: 8.8960
Evaluate side-chains
  97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue  108 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   34 MET
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain A residue   26 CYS
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  138 ARG
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  237 HIS
Chi-restraints excluded: chain A residue  249 HIS
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0370
   chunk 41 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0040
   chunk 24 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0070
   chunk 8 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.2888

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

Flipped N/Q/H residues before XYZ refinement:
L  62 ASN
A  59 ASN
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.142336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.120754 restraints weight = 6936.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.124837 restraints weight = 4196.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.127737 restraints weight = 2903.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.129805 restraints weight = 2186.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.131344 restraints weight = 1746.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5200  Z= 0.095
  Angle     :  0.500   7.681   7076  Z= 0.265
  Chirality :  0.042   0.147    796
  Planarity :  0.003   0.025    911
  Dihedral  :  4.273  30.180    716
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 21.31 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.34), residues: 651
  helix: -3.37 (0.89), residues: 23
  sheet: -0.82 (0.40), residues: 171
  loop : -0.64 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 354 
 TYR   0.013   0.001   TYR A  64 
 PHE   0.007   0.001   PHE A 400 
 TRP   0.007   0.001   TRP A 205 
 HIS   0.002   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 5186)
  covalent geometry    : angle       0.49782 ( 7048)
  SS BOND              : bond        0.00237 (   14)
  SS BOND              : angle       0.83480 (   28)
  hydrogen bonds       : bond        0.02663 (  105)
  hydrogen bonds       : angle       5.44654 (  222)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 0.211 
Fit side-chains
REVERT: H   34 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7638 (mmp)
REVERT: H   46 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6043 (mt-10)
REVERT: A  188 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6801 (mmt90)
REVERT: A  450 ILE cc_start: 0.7184 (mm) cc_final: 0.6277 (pt)
  outliers start: 26
  outliers final: 16
  residues processed: 94
  average time/residue: 0.0817
  time to fit residues: 10.0111
Evaluate side-chains
  92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  108 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   34 MET
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain A residue   26 CYS
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  249 HIS
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0170
   chunk 46 optimal weight:    0.6980
   chunk 11 optimal weight:    0.1980
   chunk 61 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
** L  33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  62 ASN
A  59 ASN
A 249 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.142247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.120236 restraints weight = 6950.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.124391 restraints weight = 4201.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.127297 restraints weight = 2910.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.129383 restraints weight = 2196.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.130884 restraints weight = 1761.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
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   0.027   5200  Z= 0.111
  Angle     :  0.513   8.062   7076  Z= 0.271
  Chirality :  0.043   0.146    796
  Planarity :  0.003   0.029    911
  Dihedral  :  4.317  30.044    716
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 20.60 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.34), residues: 651
  helix: -3.31 (0.91), residues: 23
  sheet: -0.81 (0.40), residues: 172
  loop : -0.64 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 354 
 TYR   0.025   0.001   TYR A  64 
 PHE   0.007   0.001   PHE A 400 
 TRP   0.008   0.001   TRP A 205 
 HIS   0.002   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 5186)
  covalent geometry    : angle       0.51097 ( 7048)
  SS BOND              : bond        0.00283 (   14)
  SS BOND              : angle       0.91345 (   28)
  hydrogen bonds       : bond        0.02737 (  105)
  hydrogen bonds       : angle       5.44966 (  222)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.190 
Fit side-chains
REVERT: H   34 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7618 (mmp)
REVERT: H   46 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5930 (mt-10)
REVERT: A  188 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6841 (mmt90)
REVERT: A  450 ILE cc_start: 0.7229 (mm) cc_final: 0.6311 (pt)
  outliers start: 27
  outliers final: 19
  residues processed: 90
  average time/residue: 0.0755
  time to fit residues: 8.9019
Evaluate side-chains
  94 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue  108 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   34 MET
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain A residue   26 CYS
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  249 HIS
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0050
   chunk 7 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 63 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
** L  33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  62 ASN
A  59 ASN
A 249 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.141115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.118694 restraints weight = 6946.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.122857 restraints weight = 4177.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.125830 restraints weight = 2897.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.127857 restraints weight = 2182.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.129437 restraints weight = 1767.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5200  Z= 0.130
  Angle     :  0.546  10.052   7076  Z= 0.285
  Chirality :  0.043   0.155    796
  Planarity :  0.004   0.047    911
  Dihedral  :  4.417  29.989    716
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 21.67 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.34), residues: 651
  helix: -3.33 (0.90), residues: 23
  sheet: -0.79 (0.40), residues: 172
  loop : -0.65 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 351 
 TYR   0.020   0.001   TYR A  64 
 PHE   0.008   0.001   PHE A 400 
 TRP   0.009   0.001   TRP A 205 
 HIS   0.004   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 5186)
  covalent geometry    : angle       0.54376 ( 7048)
  SS BOND              : bond        0.00274 (   14)
  SS BOND              : angle       0.90331 (   28)
  hydrogen bonds       : bond        0.02814 (  105)
  hydrogen bonds       : angle       5.55740 (  222)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 71
  time to evaluate  : 0.200 
Fit side-chains
REVERT: H   34 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7667 (mmp)
REVERT: H   46 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5925 (mt-10)
REVERT: A  188 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6822 (mmt90)
REVERT: A  450 ILE cc_start: 0.7273 (mm) cc_final: 0.6202 (pt)
  outliers start: 26
  outliers final: 19
  residues processed: 88
  average time/residue: 0.0825
  time to fit residues: 9.3917
Evaluate side-chains
  91 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue  108 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   34 MET
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain A residue   26 CYS
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  138 ARG
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  249 HIS
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 15 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** L  33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  62 ASN
A 249 HIS
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.138602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.116514 restraints weight = 7065.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.120525 restraints weight = 4276.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.123423 restraints weight = 2976.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.125482 restraints weight = 2248.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.127020 restraints weight = 1814.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5200  Z= 0.174
  Angle     :  0.585   9.860   7076  Z= 0.303
  Chirality :  0.044   0.149    796
  Planarity :  0.004   0.032    911
  Dihedral  :  4.514  19.909    715
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.85 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.34), residues: 651
  helix: -3.41 (0.88), residues: 23
  sheet: -0.85 (0.40), residues: 172
  loop : -0.72 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 351 
 TYR   0.020   0.002   TYR A  64 
 PHE   0.010   0.001   PHE A 400 
 TRP   0.012   0.002   TRP A 205 
 HIS   0.003   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 5186)
  covalent geometry    : angle       0.58271 ( 7048)
  SS BOND              : bond        0.00354 (   14)
  SS BOND              : angle       0.99515 (   28)
  hydrogen bonds       : bond        0.03111 (  105)
  hydrogen bonds       : angle       5.75627 (  222)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.145 
Fit side-chains
REVERT: H   34 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7729 (mmp)
REVERT: H   46 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5991 (mt-10)
REVERT: A  188 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6871 (mmt90)
REVERT: A  450 ILE cc_start: 0.7421 (mm) cc_final: 0.6552 (pt)
  outliers start: 24
  outliers final: 20
  residues processed: 84
  average time/residue: 0.0676
  time to fit residues: 7.6236
Evaluate side-chains
  92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   36 SER
Chi-restraints excluded: chain L residue  108 THR
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   34 MET
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  120 VAL
Chi-restraints excluded: chain A residue   26 CYS
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  138 ARG
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  249 HIS
Chi-restraints excluded: chain A residue  264 CYS
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  407 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  465 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 23 optimal weight:    0.4980
   chunk 36 optimal weight:    0.3980
   chunk 6 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0670
   chunk 15 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
L  62 ASN
A  59 ASN
A 249 HIS
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.140828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.118526 restraints weight = 7031.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.122675 restraints weight = 4235.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.125598 restraints weight = 2940.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.127691 restraints weight = 2224.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.129265 restraints weight = 1786.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5200  Z= 0.119
  Angle     :  0.548   8.855   7076  Z= 0.287
  Chirality :  0.043   0.146    796
  Planarity :  0.004   0.030    911
  Dihedral  :  4.337  19.626    715
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 21.14 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.34), residues: 651
  helix: -3.31 (0.92), residues: 23
  sheet: -0.78 (0.40), residues: 172
  loop : -0.65 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 351 
 TYR   0.019   0.001   TYR A  64 
 PHE   0.010   0.001   PHE A 400 
 TRP   0.009   0.001   TRP A 205 
 HIS   0.004   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5186)
  covalent geometry    : angle       0.54650 ( 7048)
  SS BOND              : bond        0.00261 (   14)
  SS BOND              : angle       0.88681 (   28)
  hydrogen bonds       : bond        0.02773 (  105)
  hydrogen bonds       : angle       5.58676 (  222)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1107.54 seconds
wall clock time: 19 minutes 45.95 seconds (1185.95 seconds total)