Starting phenix.real_space_refine
on Wed Jul  1 21:29:43 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7r7n_24299/07_2026/7r7n_24299.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r7n_24299/07_2026/7r7n_24299.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r7n_24299/07_2026/7r7n_24299.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r7n_24299/07_2026/7r7n_24299.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r7n_24299/07_2026/7r7n_24299.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r7n_24299/07_2026/7r7n_24299.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7r7n_24299/07_2026/7r7n_24299.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7r7n_24299/07_2026/7r7n_24299.cif"
  }
  resolution = 3.95
  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=   0.018
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      17      5.16       5
     C    1795      2.51       5
     N     481      2.21       5
     O     497      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 2790
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 735
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 4, 'TRANS': 104}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 80
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 42
    Chain: "E"
      Number of atoms: 1382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1382
          Classifications: {'peptide': 189}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 10, 'TRANS': 178}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 118
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 92
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'ASN:plan1': 4, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 61
    Chain: "L"
      Number of atoms: 635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 635
          Classifications: {'peptide': 93}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 87}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 0.93, per 1000 atoms: 0.33
  Number of scatterers: 2790
  At special positions: 0
  Unit cell: (77.7, 66.15, 76.65, 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      17     16.00
     O     497      8.00
     N     481      7.00
     C    1795      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 103 " - pdb=" SG  CYS H 108 " distance=2.12
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.09
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.21

  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
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    BETA1-6
      " NAG A   1 " - " FUC A   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A   1 " - " ASN E 343 "
  Time building additional restraints: 0.33
  Conformation dependent library (CDL) restraints added in 115.5 milliseconds
  

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  714

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 10 sheets defined
      12.3% alpha, 38.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'E' and resid 338 through 343
    Processing helix  chain 'E' and resid 349 through 353
      removed outlier: 3.808A  pdb=" N   TRP E 353 " --> pdb=" O   VAL E 350 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 370
    Processing helix  chain 'E' and resid 405 through 410
      removed outlier: 4.413A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 416 through 422
    Processing helix  chain 'E' and resid 438 through 443
    Processing helix  chain 'E' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.667A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.667A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.537A  pdb=" N   VAL E 395 " --> pdb=" O   ILE E 358 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 361 through 362
      removed outlier: 6.320A  pdb=" N   CYS E 361 " --> pdb=" O   CYS E 525 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474
    Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.603A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER L  67 " --> pdb=" O   ASP L  70 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54
      removed outlier: 6.564A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54
      removed outlier: 6.564A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)

    128 hydrogen bonds defined for protein.
    297 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: 0.42

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 808
        1.33 -     1.46: 747
        1.46 -     1.58: 1283
        1.58 -     1.71: 0
        1.71 -     1.83: 20
  Bond restraints: 2858
  Sorted by residual:
  bond pdb=" NE  ARG L  18 "
       pdb=" CZ  ARG L  18 "
    ideal  model  delta    sigma   weight residual
    1.326  1.367 -0.041 1.10e-02 8.26e+03 1.40e+01
  bond pdb=" C5  NAG A   2 "
       pdb=" O5  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.470 -0.057 2.00e-02 2.50e+03 8.07e+00
  bond pdb=" CB  ILE L   2 "
       pdb=" CG1 ILE L   2 "
    ideal  model  delta    sigma   weight residual
    1.530  1.582 -0.052 2.00e-02 2.50e+03 6.86e+00
  bond pdb=" CB  LEU E 517 "
       pdb=" CG  LEU E 517 "
    ideal  model  delta    sigma   weight residual
    1.530  1.579 -0.049 2.00e-02 2.50e+03 5.94e+00
  bond pdb=" C5  FUC A   3 "
       pdb=" O5  FUC A   3 "
    ideal  model  delta    sigma   weight residual
    1.423  1.471 -0.048 2.00e-02 2.50e+03 5.81e+00
  ... (remaining 2853 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 3270
        1.51 -     3.02: 527
        3.02 -     4.53: 68
        4.53 -     6.04: 28
        6.04 -     7.54: 14
  Bond angle restraints: 3907
  Sorted by residual:
  angle pdb=" C   GLY H  27 "
        pdb=" N   PRO H  28 "
        pdb=" CA  PRO H  28 "
      ideal   model   delta    sigma   weight residual
     119.85  127.39   -7.54 1.01e+00 9.80e-01 5.58e+01
  angle pdb=" C   SER E 383 "
        pdb=" N   PRO E 384 "
        pdb=" CA  PRO E 384 "
      ideal   model   delta    sigma   weight residual
     119.56  126.71   -7.15 1.02e+00 9.61e-01 4.91e+01
  angle pdb=" C   GLN E 498 "
        pdb=" N   PRO E 499 "
        pdb=" CA  PRO E 499 "
      ideal   model   delta    sigma   weight residual
     119.87  126.95   -7.08 1.04e+00 9.25e-01 4.63e+01
  angle pdb=" C   ALA L  43 "
        pdb=" N   PRO L  44 "
        pdb=" CA  PRO L  44 "
      ideal   model   delta    sigma   weight residual
     119.85  126.57   -6.72 1.01e+00 9.80e-01 4.42e+01
  angle pdb=" C   PHE E 490 "
        pdb=" N   PRO E 491 "
        pdb=" CA  PRO E 491 "
      ideal   model   delta    sigma   weight residual
     119.87  126.77   -6.90 1.04e+00 9.25e-01 4.40e+01
  ... (remaining 3902 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.05: 1521
       13.05 -    26.10: 74
       26.10 -    39.14: 14
       39.14 -    52.19: 9
       52.19 -    65.24: 6
  Dihedral angle restraints: 1624
    sinusoidal: 502
      harmonic: 1122
  Sorted by residual:
  dihedral pdb=" CB  CYS H 103 "
           pdb=" SG  CYS H 103 "
           pdb=" SG  CYS H 108 "
           pdb=" CB  CYS H 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -151.24   65.24     1      1.00e+01 1.00e-02 5.58e+01
  dihedral pdb=" CB  CYS E 391 "
           pdb=" SG  CYS E 391 "
           pdb=" SG  CYS E 525 "
           pdb=" CB  CYS E 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.49   47.51     1      1.00e+01 1.00e-02 3.12e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   62.52   30.48     1      1.00e+01 1.00e-02 1.33e+01
  ... (remaining 1621 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.057: 306
       0.057 -    0.114: 93
       0.114 -    0.171: 26
       0.171 -    0.228: 9
       0.228 -    0.285: 6
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.53    0.13 2.00e-02 2.50e+03 4.12e+01
  chirality pdb=" C1  FUC A   3 "
            pdb=" O6  NAG A   1 "
            pdb=" C2  FUC A   3 "
            pdb=" O5  FUC A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.44    0.04 2.00e-02 2.50e+03 4.68e+00
  chirality pdb=" C2  NAG A   2 "
            pdb=" C1  NAG A   2 "
            pdb=" C3  NAG A   2 "
            pdb=" N2  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.78    0.29 2.00e-01 2.50e+01 2.03e+00
  ... (remaining 437 not shown)

  Planarity restraints: 505
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR E 489 "    0.008 2.00e-02 2.50e+03   1.63e-02 2.66e+00
        pdb=" C   TYR E 489 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   TYR E 489 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE E 490 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  92 "   -0.021 2.00e-02 2.50e+03   1.12e-02 2.53e+00
        pdb=" CG  TYR L  92 "    0.006 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  92 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  92 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  92 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  92 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  92 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR L  92 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 449 "    0.019 2.00e-02 2.50e+03   1.06e-02 2.23e+00
        pdb=" CG  TYR E 449 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 449 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 449 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 449 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 449 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 449 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR E 449 "    0.017 2.00e-02 2.50e+03
  ... (remaining 502 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 1515
        3.02 -     3.49: 2477
        3.49 -     3.96: 4310
        3.96 -     4.43: 4896
        4.43 -     4.90: 7917
  Nonbonded interactions: 21115
  Sorted by model distance:
  nonbonded pdb=" N   ASP E 428 "
            pdb=" OD1 ASP E 428 "
     model   vdw
     2.553 3.120
  nonbonded pdb=" N   LYS E 462 "
            pdb=" O   LYS E 462 "
     model   vdw
     2.609 2.496
  nonbonded pdb=" N   GLN L   3 "
            pdb=" OE1 GLN L   3 "
     model   vdw
     2.616 3.120
  nonbonded pdb=" N   THR H  76 "
            pdb=" N   SER H  77 "
     model   vdw
     2.623 2.560
  nonbonded pdb=" N   ALA E 372 "
            pdb=" N   SER E 373 "
     model   vdw
     2.627 2.560
  ... (remaining 21110 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.480
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.990
  Find NCS groups from input model:        0.030
  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:   13.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
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      :  0.011   0.177   2868  Z= 0.604
  Angle     :  1.277   9.127   3930  Z= 0.844
  Chirality :  0.069   0.285    440
  Planarity :  0.005   0.016    504
  Dihedral  :  9.475  63.153    889
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 0.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  0.90 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.43), residues: 373
  helix: -4.27 (0.43), residues: 26
  sheet:  0.66 (0.46), residues: 126
  loop :  0.27 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 454 
 TYR   0.021   0.004   TYR L  92 
 PHE   0.016   0.003   PHE L  98 
 TRP   0.016   0.005   TRP L  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01027 /  0.57 ( 2858)
  covalent geometry    : angle       1.24490 /  0.84 ( 3907)
  SS BOND              : bond        0.07783 /  2.80 (    7)
  SS BOND              : angle       4.71542 /  2.57 (   14)
  hydrogen bonds       : bond        0.15942 / 11.55 (  106)
  hydrogen bonds       : angle       9.61620 /  6.38 (  297)
  link_BETA1-4         : bond        0.06871 /  3.62 (    1)
  link_BETA1-4         : angle       2.84603 /  1.49 (    3)
  link_BETA1-6         : bond        0.04724 /  2.49 (    1)
  link_BETA1-6         : angle       1.54020 /  0.83 (    3)
  link_NAG-ASN         : bond        0.05761 /  3.03 (    1)
  link_NAG-ASN         : angle       2.26738 /  1.17 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: H    3 GLN cc_start: 0.8454 (mp10) cc_final: 0.8035 (tp40)
REVERT: E  467 ASP cc_start: 0.7653 (t0) cc_final: 0.6608 (p0)
REVERT: E  513 LEU cc_start: 0.8949 (mt) cc_final: 0.8629 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 100
  average time/residue: 0.0850
  time to fit residues: 9.8033
Evaluate side-chains
  57 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  109 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    0.0170
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0970
   chunk 22 optimal weight:    0.2980
   chunk 13 optimal weight:    0.4980
   overall best weight:    0.2416

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H   6 GLN
H 118 GLN
L   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.101977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.093772 restraints weight = 7091.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.095665 restraints weight = 4134.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.097005 restraints weight = 2679.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.097887 restraints weight = 1880.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.098577 restraints weight = 1436.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   2868  Z= 0.145
  Angle     :  0.656  10.394   3930  Z= 0.340
  Chirality :  0.048   0.195    440
  Planarity :  0.004   0.027    504
  Dihedral  :  5.168  50.045    425
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 15.70 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.42), residues: 373
  helix: -3.56 (0.78), residues: 26
  sheet:  0.79 (0.45), residues: 129
  loop :  0.15 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 403 
 TYR   0.018   0.002   TYR H  95 
 PHE   0.028   0.002   PHE H  29 
 TRP   0.012   0.001   TRP H  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.14 ( 2858)
  covalent geometry    : angle       0.64602 /  0.34 ( 3907)
  SS BOND              : bond        0.00880 /  0.47 (    7)
  SS BOND              : angle       1.77655 /  0.95 (   14)
  hydrogen bonds       : bond        0.03666 /  2.37 (  106)
  hydrogen bonds       : angle       6.87387 /  4.62 (  297)
  link_BETA1-4         : bond        0.00577 /  0.30 (    1)
  link_BETA1-4         : angle       1.11139 /  0.55 (    3)
  link_BETA1-6         : bond        0.00514 /  0.27 (    1)
  link_BETA1-6         : angle       1.79646 /  0.86 (    3)
  link_NAG-ASN         : bond        0.00490 /  0.26 (    1)
  link_NAG-ASN         : angle       1.21762 /  0.59 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: E  512 VAL cc_start: 0.9435 (t) cc_final: 0.9225 (t)
REVERT: E  513 LEU cc_start: 0.9020 (mt) cc_final: 0.8760 (tt)
REVERT: L   49 TYR cc_start: 0.8044 (p90) cc_final: 0.7715 (p90)
  outliers start: 14
  outliers final: 10
  residues processed: 67
  average time/residue: 0.0534
  time to fit residues: 4.4825
Evaluate side-chains
  58 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain E residue  349 SER
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  392 PHE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  517 LEU
Chi-restraints excluded: chain L residue   88 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 35 optimal weight:    0.0670
   chunk 16 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0970
   chunk 26 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0980
   chunk 8 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.3516

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.097942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.089642 restraints weight = 7322.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.091478 restraints weight = 4258.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.092807 restraints weight = 2777.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.093758 restraints weight = 1968.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.094413 restraints weight = 1490.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   2868  Z= 0.161
  Angle     :  0.610   5.970   3930  Z= 0.316
  Chirality :  0.045   0.139    440
  Planarity :  0.004   0.025    504
  Dihedral  :  4.897  43.041    425
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  7.17 %
    Allowed  : 17.94 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.43), residues: 373
  helix: -3.21 (0.92), residues: 26
  sheet:  1.01 (0.47), residues: 118
  loop : -0.01 (0.40), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 403 
 TYR   0.013   0.002   TYR H  95 
 PHE   0.031   0.002   PHE E 374 
 TRP   0.012   0.001   TRP H  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.16 ( 2858)
  covalent geometry    : angle       0.59978 /  0.31 ( 3907)
  SS BOND              : bond        0.00667 /  0.35 (    7)
  SS BOND              : angle       1.57252 /  0.89 (   14)
  hydrogen bonds       : bond        0.03308 /  2.14 (  106)
  hydrogen bonds       : angle       6.37357 /  4.34 (  297)
  link_BETA1-4         : bond        0.00570 /  0.30 (    1)
  link_BETA1-4         : angle       1.28864 /  0.67 (    3)
  link_BETA1-6         : bond        0.00213 /  0.11 (    1)
  link_BETA1-6         : angle       1.70317 /  0.80 (    3)
  link_NAG-ASN         : bond        0.00170 /  0.09 (    1)
  link_NAG-ASN         : angle       1.71728 /  0.82 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: E  512 VAL cc_start: 0.9483 (t) cc_final: 0.9156 (m)
REVERT: E  513 LEU cc_start: 0.9028 (mt) cc_final: 0.8689 (tt)
REVERT: L   49 TYR cc_start: 0.8076 (p90) cc_final: 0.7516 (p90)
  outliers start: 16
  outliers final: 13
  residues processed: 65
  average time/residue: 0.0422
  time to fit residues: 3.6098
Evaluate side-chains
  62 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue  103 CYS
Chi-restraints excluded: chain H residue  108 CYS
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  368 LEU
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  392 PHE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  517 LEU
Chi-restraints excluded: chain L residue   88 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 32 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.094872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.087180 restraints weight = 7321.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.088912 restraints weight = 4278.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.090128 restraints weight = 2796.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.090982 restraints weight = 1981.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.091631 restraints weight = 1502.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079   2868  Z= 0.195
  Angle     :  0.635   6.106   3930  Z= 0.329
  Chirality :  0.045   0.140    440
  Planarity :  0.004   0.029    504
  Dihedral  :  4.964  39.522    425
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  7.17 %
    Allowed  : 17.04 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.43), residues: 373
  helix: -2.80 (1.04), residues: 26
  sheet:  0.75 (0.46), residues: 129
  loop : -0.28 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 403 
 TYR   0.014   0.001   TYR H  95 
 PHE   0.023   0.002   PHE H  29 
 TRP   0.013   0.001   TRP H  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00454 /  0.19 ( 2858)
  covalent geometry    : angle       0.62339 /  0.32 ( 3907)
  SS BOND              : bond        0.00692 /  0.34 (    7)
  SS BOND              : angle       1.67416 /  0.95 (   14)
  hydrogen bonds       : bond        0.03179 /  2.04 (  106)
  hydrogen bonds       : angle       5.99225 /  4.10 (  297)
  link_BETA1-4         : bond        0.00698 /  0.37 (    1)
  link_BETA1-4         : angle       1.54170 /  0.80 (    3)
  link_BETA1-6         : bond        0.00408 /  0.21 (    1)
  link_BETA1-6         : angle       1.79865 /  0.83 (    3)
  link_NAG-ASN         : bond        0.00085 /  0.04 (    1)
  link_NAG-ASN         : angle       2.05208 /  0.98 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 49
  time to evaluate  : 0.129 
Fit side-chains
REVERT: E  442 ASP cc_start: 0.8669 (t0) cc_final: 0.8464 (t0)
REVERT: E  513 LEU cc_start: 0.9075 (mt) cc_final: 0.8739 (tt)
REVERT: L   49 TYR cc_start: 0.8102 (p90) cc_final: 0.7663 (p90)
  outliers start: 16
  outliers final: 14
  residues processed: 60
  average time/residue: 0.0408
  time to fit residues: 3.3141
Evaluate side-chains
  62 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  103 CYS
Chi-restraints excluded: chain H residue  108 CYS
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  392 PHE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  517 LEU
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   88 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0020
   chunk 1 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 27 optimal weight:    0.2980
   overall best weight:    0.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H   6 GLN
H 118 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.091982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.083874 restraints weight = 7373.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.085673 restraints weight = 4216.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.086961 restraints weight = 2714.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.087893 restraints weight = 1906.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.088523 restraints weight = 1432.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.4419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078   2868  Z= 0.208
  Angle     :  0.640   6.525   3930  Z= 0.331
  Chirality :  0.046   0.139    440
  Planarity :  0.004   0.028    504
  Dihedral  :  5.070  38.992    425
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  7.62 %
    Allowed  : 20.18 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.42), residues: 373
  helix: -2.59 (1.07), residues: 26
  sheet:  1.09 (0.48), residues: 118
  loop : -0.68 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 457 
 TYR   0.012   0.001   TYR E 473 
 PHE   0.020   0.002   PHE H  29 
 TRP   0.017   0.002   TRP H  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00477 /  0.21 ( 2858)
  covalent geometry    : angle       0.63037 /  0.33 ( 3907)
  SS BOND              : bond        0.00666 /  0.29 (    7)
  SS BOND              : angle       1.34218 /  0.78 (   14)
  hydrogen bonds       : bond        0.03203 /  2.08 (  106)
  hydrogen bonds       : angle       6.04338 /  4.11 (  297)
  link_BETA1-4         : bond        0.00736 /  0.39 (    1)
  link_BETA1-4         : angle       1.80764 /  0.93 (    3)
  link_BETA1-6         : bond        0.00094 /  0.05 (    1)
  link_BETA1-6         : angle       1.92960 /  0.89 (    3)
  link_NAG-ASN         : bond        0.00106 /  0.06 (    1)
  link_NAG-ASN         : angle       2.03846 /  0.98 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: E  513 LEU cc_start: 0.9102 (mt) cc_final: 0.8721 (tt)
REVERT: L   49 TYR cc_start: 0.8241 (p90) cc_final: 0.7814 (p90)
  outliers start: 17
  outliers final: 14
  residues processed: 63
  average time/residue: 0.0381
  time to fit residues: 3.2490
Evaluate side-chains
  63 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  103 CYS
Chi-restraints excluded: chain H residue  108 CYS
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  391 CYS
Chi-restraints excluded: chain E residue  392 PHE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  517 LEU
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   88 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 23 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   chunk 0 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 24 optimal weight:    0.4980
   chunk 30 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0670
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.4518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 118 GLN
L  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.093074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.085903 restraints weight = 7383.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.087496 restraints weight = 4342.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.088612 restraints weight = 2853.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.089367 restraints weight = 2025.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.089955 restraints weight = 1551.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.4656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   2868  Z= 0.181
  Angle     :  0.623   5.989   3930  Z= 0.319
  Chirality :  0.045   0.133    440
  Planarity :  0.004   0.026    504
  Dihedral  :  4.647  23.253    423
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 22.42 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.42), residues: 373
  helix: -2.48 (0.94), residues: 33
  sheet:  0.98 (0.48), residues: 118
  loop : -0.80 (0.39), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 457 
 TYR   0.013   0.001   TYR E 473 
 PHE   0.019   0.002   PHE H  29 
 TRP   0.016   0.002   TRP H  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.18 ( 2858)
  covalent geometry    : angle       0.61393 /  0.32 ( 3907)
  SS BOND              : bond        0.00598 /  0.27 (    7)
  SS BOND              : angle       1.22427 /  0.71 (   14)
  hydrogen bonds       : bond        0.03137 /  2.04 (  106)
  hydrogen bonds       : angle       6.01192 /  4.10 (  297)
  link_BETA1-4         : bond        0.00728 /  0.38 (    1)
  link_BETA1-4         : angle       1.65144 /  0.85 (    3)
  link_BETA1-6         : bond        0.00199 /  0.10 (    1)
  link_BETA1-6         : angle       1.79993 /  0.84 (    3)
  link_NAG-ASN         : bond        0.00128 /  0.07 (    1)
  link_NAG-ASN         : angle       1.97192 /  0.95 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.8271 (t80) cc_final: 0.7795 (t80)
REVERT: E  513 LEU cc_start: 0.9088 (mt) cc_final: 0.8752 (tt)
REVERT: L   49 TYR cc_start: 0.8169 (p90) cc_final: 0.7794 (p90)
  outliers start: 15
  outliers final: 13
  residues processed: 67
  average time/residue: 0.0543
  time to fit residues: 4.6169
Evaluate side-chains
  64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  103 CYS
Chi-restraints excluded: chain H residue  108 CYS
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  391 CYS
Chi-restraints excluded: chain E residue  392 PHE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  517 LEU
Chi-restraints excluded: chain E residue  523 THR
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   88 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 0 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0870
   chunk 29 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.4558

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.091663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.084203 restraints weight = 7312.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.085789 restraints weight = 4245.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.086926 restraints weight = 2772.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.087760 restraints weight = 1989.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.088370 restraints weight = 1515.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.4927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   2868  Z= 0.186
  Angle     :  0.654   6.856   3930  Z= 0.333
  Chirality :  0.045   0.132    440
  Planarity :  0.004   0.026    504
  Dihedral  :  4.724  27.023    423
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 21.52 %
    Favored  : 73.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.43), residues: 373
  helix: -2.27 (1.00), residues: 33
  sheet:  1.00 (0.47), residues: 120
  loop : -0.90 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 457 
 TYR   0.015   0.001   TYR E 473 
 PHE   0.013   0.002   PHE E 392 
 TRP   0.014   0.001   TRP H  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00439 /  0.19 ( 2858)
  covalent geometry    : angle       0.64041 /  0.33 ( 3907)
  SS BOND              : bond        0.00595 /  0.27 (    7)
  SS BOND              : angle       1.88384 /  1.17 (   14)
  hydrogen bonds       : bond        0.03066 /  2.00 (  106)
  hydrogen bonds       : angle       5.94721 /  4.08 (  297)
  link_BETA1-4         : bond        0.00613 /  0.32 (    1)
  link_BETA1-4         : angle       1.58860 /  0.82 (    3)
  link_BETA1-6         : bond        0.00181 /  0.10 (    1)
  link_BETA1-6         : angle       1.82339 /  0.85 (    3)
  link_NAG-ASN         : bond        0.00177 /  0.09 (    1)
  link_NAG-ASN         : angle       1.73528 /  0.83 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: E  513 LEU cc_start: 0.9091 (mt) cc_final: 0.8746 (tt)
REVERT: L   49 TYR cc_start: 0.8138 (p90) cc_final: 0.7766 (p90)
  outliers start: 11
  outliers final: 11
  residues processed: 58
  average time/residue: 0.0375
  time to fit residues: 2.9269
Evaluate side-chains
  62 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  103 CYS
Chi-restraints excluded: chain H residue  108 CYS
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  392 PHE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  517 LEU
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   88 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0980
   overall best weight:    0.5180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.091554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.083993 restraints weight = 7623.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.085637 restraints weight = 4415.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.086820 restraints weight = 2877.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.087669 restraints weight = 2044.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.088237 restraints weight = 1551.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.5130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   2868  Z= 0.203
  Angle     :  0.676   6.330   3930  Z= 0.347
  Chirality :  0.046   0.137    440
  Planarity :  0.004   0.026    504
  Dihedral  :  4.790  26.004    423
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 23.77 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.43), residues: 373
  helix: -2.41 (0.92), residues: 33
  sheet:  1.01 (0.47), residues: 119
  loop : -0.92 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 466 
 TYR   0.012   0.001   TYR E 473 
 PHE   0.014   0.002   PHE H  29 
 TRP   0.018   0.002   TRP H  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00480 /  0.20 ( 2858)
  covalent geometry    : angle       0.66536 /  0.34 ( 3907)
  SS BOND              : bond        0.00599 /  0.27 (    7)
  SS BOND              : angle       1.71647 /  1.03 (   14)
  hydrogen bonds       : bond        0.03107 /  2.03 (  106)
  hydrogen bonds       : angle       5.95818 /  4.09 (  297)
  link_BETA1-4         : bond        0.00588 /  0.31 (    1)
  link_BETA1-4         : angle       1.68435 /  0.87 (    3)
  link_BETA1-6         : bond        0.00031 /  0.02 (    1)
  link_BETA1-6         : angle       1.76655 /  0.82 (    3)
  link_NAG-ASN         : bond        0.00177 /  0.09 (    1)
  link_NAG-ASN         : angle       1.72078 /  0.82 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: E  513 LEU cc_start: 0.9103 (mt) cc_final: 0.8755 (tt)
REVERT: L   49 TYR cc_start: 0.8208 (p90) cc_final: 0.7914 (p90)
  outliers start: 11
  outliers final: 11
  residues processed: 60
  average time/residue: 0.0436
  time to fit residues: 3.4249
Evaluate side-chains
  62 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  103 CYS
Chi-restraints excluded: chain H residue  108 CYS
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  392 PHE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  517 LEU
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   88 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    0.3980
   chunk 17 optimal weight:    0.0170
   chunk 11 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 21 optimal weight:    0.4980
   overall best weight:    0.4218

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.092030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.084464 restraints weight = 7576.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.086114 restraints weight = 4385.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.087301 restraints weight = 2856.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.088131 restraints weight = 2036.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.088751 restraints weight = 1554.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.5232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   2868  Z= 0.173
  Angle     :  0.650   6.242   3930  Z= 0.329
  Chirality :  0.045   0.129    440
  Planarity :  0.004   0.027    504
  Dihedral  :  4.618  24.859    423
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 22.87 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.42), residues: 373
  helix: -3.30 (0.81), residues: 33
  sheet:  0.93 (0.46), residues: 119
  loop : -0.94 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 403 
 TYR   0.011   0.001   TYR E 473 
 PHE   0.012   0.002   PHE E 392 
 TRP   0.016   0.002   TRP H  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.17 ( 2858)
  covalent geometry    : angle       0.64147 /  0.33 ( 3907)
  SS BOND              : bond        0.00561 /  0.25 (    7)
  SS BOND              : angle       1.38405 /  0.83 (   14)
  hydrogen bonds       : bond        0.02962 /  1.93 (  106)
  hydrogen bonds       : angle       5.87703 /  4.03 (  297)
  link_BETA1-4         : bond        0.00598 /  0.31 (    1)
  link_BETA1-4         : angle       1.61783 /  0.83 (    3)
  link_BETA1-6         : bond        0.00201 /  0.11 (    1)
  link_BETA1-6         : angle       1.66717 /  0.78 (    3)
  link_NAG-ASN         : bond        0.00216 /  0.11 (    1)
  link_NAG-ASN         : angle       1.58226 /  0.75 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: E  513 LEU cc_start: 0.9134 (mt) cc_final: 0.8750 (tt)
REVERT: L   49 TYR cc_start: 0.8195 (p90) cc_final: 0.7926 (p90)
  outliers start: 12
  outliers final: 12
  residues processed: 61
  average time/residue: 0.0429
  time to fit residues: 3.4444
Evaluate side-chains
  64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  103 CYS
Chi-restraints excluded: chain H residue  108 CYS
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  392 PHE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  517 LEU
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   32 TYR
Chi-restraints excluded: chain L residue   88 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0020
   chunk 30 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0870
   chunk 3 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0270
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.3624

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.092706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.084971 restraints weight = 7546.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.086618 restraints weight = 4372.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.087863 restraints weight = 2872.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.088665 restraints weight = 2036.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.089324 restraints weight = 1564.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.5333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   2868  Z= 0.154
  Angle     :  0.639   6.347   3930  Z= 0.321
  Chirality :  0.045   0.130    440
  Planarity :  0.004   0.026    504
  Dihedral  :  4.548  24.028    423
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 23.32 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.43), residues: 373
  helix: -3.34 (0.78), residues: 33
  sheet:  0.95 (0.47), residues: 113
  loop : -0.86 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 403 
 TYR   0.011   0.001   TYR E 473 
 PHE   0.012   0.002   PHE E 392 
 TRP   0.015   0.002   TRP H  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00365 /  0.15 ( 2858)
  covalent geometry    : angle       0.63086 /  0.32 ( 3907)
  SS BOND              : bond        0.00523 /  0.24 (    7)
  SS BOND              : angle       1.45776 /  0.86 (   14)
  hydrogen bonds       : bond        0.02869 /  1.86 (  106)
  hydrogen bonds       : angle       5.78897 /  3.98 (  297)
  link_BETA1-4         : bond        0.00455 /  0.24 (    1)
  link_BETA1-4         : angle       1.54672 /  0.79 (    3)
  link_BETA1-6         : bond        0.00162 /  0.09 (    1)
  link_BETA1-6         : angle       1.60569 /  0.75 (    3)
  link_NAG-ASN         : bond        0.00219 /  0.12 (    1)
  link_NAG-ASN         : angle       1.47535 /  0.70 (    3)

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

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

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  746 Ramachandran restraints generated.
    373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: E  512 VAL cc_start: 0.9464 (t) cc_final: 0.9181 (m)
REVERT: E  513 LEU cc_start: 0.9132 (mt) cc_final: 0.8763 (tt)
REVERT: L   49 TYR cc_start: 0.8135 (p90) cc_final: 0.7865 (p90)
  outliers start: 12
  outliers final: 12
  residues processed: 61
  average time/residue: 0.0419
  time to fit residues: 3.4102
Evaluate side-chains
  62 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  103 CYS
Chi-restraints excluded: chain H residue  108 CYS
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  392 PHE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  517 LEU
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   32 TYR
Chi-restraints excluded: chain L residue   88 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0570
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0980
   chunk 27 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.3898

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.092819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.085157 restraints weight = 7345.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.086812 restraints weight = 4284.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.087943 restraints weight = 2808.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.088810 restraints weight = 2028.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.089400 restraints weight = 1539.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.5417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   2868  Z= 0.164
  Angle     :  0.653   7.530   3930  Z= 0.327
  Chirality :  0.046   0.152    440
  Planarity :  0.004   0.027    504
  Dihedral  :  4.509  23.419    423
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 21.97 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.42), residues: 373
  helix: -3.37 (0.77), residues: 33
  sheet:  0.91 (0.47), residues: 113
  loop : -0.91 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 403 
 TYR   0.012   0.001   TYR H  95 
 PHE   0.012   0.002   PHE E 342 
 TRP   0.014   0.002   TRP H  47 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.16 ( 2858)
  covalent geometry    : angle       0.64647 /  0.32 ( 3907)
  SS BOND              : bond        0.00542 /  0.25 (    7)
  SS BOND              : angle       1.25819 /  0.75 (   14)
  hydrogen bonds       : bond        0.02825 /  1.83 (  106)
  hydrogen bonds       : angle       5.82404 /  4.02 (  297)
  link_BETA1-4         : bond        0.00523 /  0.28 (    1)
  link_BETA1-4         : angle       1.51206 /  0.78 (    3)
  link_BETA1-6         : bond        0.00225 /  0.12 (    1)
  link_BETA1-6         : angle       1.65714 /  0.77 (    3)
  link_NAG-ASN         : bond        0.00251 /  0.13 (    1)
  link_NAG-ASN         : angle       1.30322 /  0.62 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 803.83 seconds
wall clock time: 14 minutes 31.75 seconds (871.75 seconds total)