Starting phenix.real_space_refine
on Fri Aug 22 13:03:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r7n_24299/08_2025/7r7n_24299.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r7n_24299/08_2025/7r7n_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_24299/08_2025/7r7n_24299.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r7n_24299/08_2025/7r7n_24299.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r7n_24299/08_2025/7r7n_24299.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r7n_24299/08_2025/7r7n_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-2.0-5787/lib/python3.9/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 dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 0.96, per 1000 atoms: 0.34
  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: 0.28
  Conformation dependent library (CDL) restraints added in 124.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.12
  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: 0.45

  Time building geometry restraints manager: 0.37 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: 1577
       13.05 -    26.10: 77
       26.10 -    39.14: 14
       39.14 -    52.19: 9
       52.19 -    65.24: 6
  Dihedral angle restraints: 1683
    sinusoidal: 561
      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 1680 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.040
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.640
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
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  :  9.309  63.153    948
  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 aren 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
  covalent geometry    : bond        0.01027 ( 2858)
  covalent geometry    : angle       1.24490 ( 3907)
  SS BOND              : bond        0.07783 (    7)
  SS BOND              : angle       4.71542 (   14)
  hydrogen bonds       : bond        0.15942 (  106)
  hydrogen bonds       : angle       9.61620 (  297)
  link_BETA1-4         : bond        0.06871 (    1)
  link_BETA1-4         : angle       2.84603 (    3)
  link_BETA1-6         : bond        0.04724 (    1)
  link_BETA1-6         : angle       1.54020 (    3)
  link_NAG-ASN         : bond        0.05761 (    1)
  link_NAG-ASN         : angle       2.26738 (    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  : 0.108 
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: 0.0848
  time to fit residues: 9.7124
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  : 0.082 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 118 GLN
L   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.101916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.093747 restraints weight = 7090.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.095620 restraints weight = 4124.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.096957 restraints weight = 2678.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.097815 restraints weight = 1882.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.098529 restraints weight = 1440.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   2868  Z= 0.151
  Angle     :  0.656  10.503   3930  Z= 0.339
  Chirality :  0.047   0.202    440
  Planarity :  0.004   0.027    504
  Dihedral  :  5.044  49.649    484
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 16.14 %
    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 aren not related in a simple way.
  whole:  0.08 (0.42), residues: 373
  helix: -3.61 (0.75), residues: 26
  sheet:  0.81 (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   0.017   0.002   TYR H  95 
 PHE   0.027   0.002   PHE H  29 
 TRP   0.012   0.001   TRP H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 2858)
  covalent geometry    : angle       0.64284 ( 3907)
  SS BOND              : bond        0.00705 (    7)
  SS BOND              : angle       2.03541 (   14)
  hydrogen bonds       : bond        0.03758 (  106)
  hydrogen bonds       : angle       6.84791 (  297)
  link_BETA1-4         : bond        0.00633 (    1)
  link_BETA1-4         : angle       1.43026 (    3)
  link_BETA1-6         : bond        0.00278 (    1)
  link_BETA1-6         : angle       1.66505 (    3)
  link_NAG-ASN         : bond        0.00186 (    1)
  link_NAG-ASN         : angle       1.16340 (    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
  73 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.105 
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: 0.8755 (tt)
REVERT: L   49 TYR cc_start: 0.8045 (p90) cc_final: 0.7707 (p90)
  outliers start: 13
  outliers final: 10
  residues processed: 67
  average time/residue: 0.0531
  time to fit residues: 4.4364
Evaluate side-chains
  59 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 16 optimal weight:    0.2980
   chunk 34 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   chunk 14 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 15 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3443 r_free = 0.3443 target = 0.097184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.088921 restraints weight = 7339.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.090758 restraints weight = 4281.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.092090 restraints weight = 2783.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.092968 restraints weight = 1960.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.093670 restraints weight = 1500.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   2868  Z= 0.180
  Angle     :  0.629   6.190   3930  Z= 0.327
  Chirality :  0.045   0.139    440
  Planarity :  0.004   0.026    504
  Dihedral  :  5.042  43.468    484
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  7.62 %
    Allowed  : 17.94 %
    Favored  : 74.44 %
  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 aren not related in a simple way.
  whole:  0.03 (0.43), residues: 373
  helix: -3.18 (0.90), residues: 26
  sheet:  0.99 (0.47), residues: 119
  loop : -0.05 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 403 
 TYR   0.013   0.002   TYR H  95 
 PHE   0.037   0.002   PHE E 374 
 TRP   0.013   0.001   TRP H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 2858)
  covalent geometry    : angle       0.61740 ( 3907)
  SS BOND              : bond        0.00691 (    7)
  SS BOND              : angle       1.69632 (   14)
  hydrogen bonds       : bond        0.03364 (  106)
  hydrogen bonds       : angle       6.41051 (  297)
  link_BETA1-4         : bond        0.00600 (    1)
  link_BETA1-4         : angle       1.72629 (    3)
  link_BETA1-6         : bond        0.00274 (    1)
  link_BETA1-6         : angle       1.83214 (    3)
  link_NAG-ASN         : bond        0.00172 (    1)
  link_NAG-ASN         : angle       1.64540 (    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
  73 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: E  512 VAL cc_start: 0.9478 (t) cc_final: 0.9198 (m)
REVERT: E  513 LEU cc_start: 0.9047 (mt) cc_final: 0.8701 (tt)
REVERT: L   49 TYR cc_start: 0.8094 (p90) cc_final: 0.7611 (p90)
  outliers start: 17
  outliers final: 15
  residues processed: 65
  average time/residue: 0.0433
  time to fit residues: 3.6894
Evaluate side-chains
  64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
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  349 SER
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  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 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:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 28 optimal weight:    0.2980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3352 r_free = 0.3352 target = 0.091863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.084073 restraints weight = 7372.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.085782 restraints weight = 4326.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.087050 restraints weight = 2837.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.087922 restraints weight = 2000.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.088519 restraints weight = 1510.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.4176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.088   2868  Z= 0.234
  Angle     :  0.679   6.348   3930  Z= 0.354
  Chirality :  0.046   0.141    440
  Planarity :  0.005   0.032    504
  Dihedral  :  5.796  40.623    484
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  7.17 %
    Allowed  : 17.49 %
    Favored  : 75.34 %
  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 aren not related in a simple way.
  whole: -0.32 (0.42), residues: 373
  helix: -2.72 (1.05), residues: 26
  sheet:  0.95 (0.47), residues: 120
  loop : -0.54 (0.39), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 457 
 TYR   0.015   0.002   TYR E 423 
 PHE   0.025   0.003   PHE E 374 
 TRP   0.018   0.002   TRP H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 2858)
  covalent geometry    : angle       0.66661 ( 3907)
  SS BOND              : bond        0.00693 (    7)
  SS BOND              : angle       1.58529 (   14)
  hydrogen bonds       : bond        0.03420 (  106)
  hydrogen bonds       : angle       6.12521 (  297)
  link_BETA1-4         : bond        0.00689 (    1)
  link_BETA1-4         : angle       2.24266 (    3)
  link_BETA1-6         : bond        0.00085 (    1)
  link_BETA1-6         : angle       2.13773 (    3)
  link_NAG-ASN         : bond        0.00139 (    1)
  link_NAG-ASN         : angle       2.03010 (    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
  67 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 51
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: E  442 ASP cc_start: 0.8814 (t0) cc_final: 0.8606 (t0)
REVERT: E  513 LEU cc_start: 0.9120 (mt) cc_final: 0.8750 (tt)
REVERT: L   49 TYR cc_start: 0.8162 (p90) cc_final: 0.7751 (p90)
  outliers start: 16
  outliers final: 14
  residues processed: 61
  average time/residue: 0.0367
  time to fit residues: 3.0331
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  : 0.100 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 34 optimal weight:    0.0670
   chunk 36 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0060
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    0.2980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.4534

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3386 r_free = 0.3386 target = 0.093371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.086233 restraints weight = 7341.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.087778 restraints weight = 4409.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.088880 restraints weight = 2944.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.089437 restraints weight = 2121.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.090189 restraints weight = 1700.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.4436

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= 0.176
  Angle     :  0.621   6.086   3930  Z= 0.317
  Chirality :  0.046   0.138    440
  Planarity :  0.004   0.032    504
  Dihedral  :  5.378  39.447    484
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  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 aren not related in a simple way.
  whole: -0.36 (0.43), residues: 373
  helix: -2.45 (1.10), residues: 26
  sheet:  1.09 (0.48), residues: 118
  loop : -0.71 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 403 
 TYR   0.011   0.001   TYR E 423 
 PHE   0.021   0.002   PHE H  29 
 TRP   0.014   0.002   TRP H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 2858)
  covalent geometry    : angle       0.61181 ( 3907)
  SS BOND              : bond        0.00638 (    7)
  SS BOND              : angle       1.23670 (   14)
  hydrogen bonds       : bond        0.03097 (  106)
  hydrogen bonds       : angle       6.04230 (  297)
  link_BETA1-4         : bond        0.00448 (    1)
  link_BETA1-4         : angle       2.29947 (    3)
  link_BETA1-6         : bond        0.00103 (    1)
  link_BETA1-6         : angle       1.78761 (    3)
  link_NAG-ASN         : bond        0.00233 (    1)
  link_NAG-ASN         : angle       1.40658 (    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
  73 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
REVERT: E  513 LEU cc_start: 0.9086 (mt) cc_final: 0.8717 (tt)
REVERT: L   49 TYR cc_start: 0.8203 (p90) cc_final: 0.7781 (p90)
  outliers start: 17
  outliers final: 12
  residues processed: 66
  average time/residue: 0.0428
  time to fit residues: 3.5994
Evaluate side-chains
  60 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    0.5980
   chunk 27 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
L  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.090280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.082856 restraints weight = 7527.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.084410 restraints weight = 4438.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.085566 restraints weight = 2933.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.086376 restraints weight = 2107.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.086919 restraints weight = 1606.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.4846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.098   2868  Z= 0.252
  Angle     :  0.705   6.376   3930  Z= 0.365
  Chirality :  0.047   0.138    440
  Planarity :  0.005   0.033    504
  Dihedral  :  5.746  30.471    482
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 22.42 %
    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 aren not related in a simple way.
  whole: -0.61 (0.42), residues: 373
  helix: -2.22 (1.15), residues: 26
  sheet:  0.93 (0.47), residues: 120
  loop : -0.96 (0.39), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 457 
 TYR   0.013   0.002   TYR H  95 
 PHE   0.015   0.002   PHE E 392 
 TRP   0.017   0.002   TRP H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 ( 2858)
  covalent geometry    : angle       0.69067 ( 3907)
  SS BOND              : bond        0.00630 (    7)
  SS BOND              : angle       1.80209 (   14)
  hydrogen bonds       : bond        0.03466 (  106)
  hydrogen bonds       : angle       6.20941 (  297)
  link_BETA1-4         : bond        0.00552 (    1)
  link_BETA1-4         : angle       2.32831 (    3)
  link_BETA1-6         : bond        0.00159 (    1)
  link_BETA1-6         : angle       2.12668 (    3)
  link_NAG-ASN         : bond        0.00052 (    1)
  link_NAG-ASN         : angle       1.98335 (    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
  69 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.8155 (t80) cc_final: 0.7924 (t80)
REVERT: H  118 GLN cc_start: 0.7979 (tp40) cc_final: 0.7774 (tp40)
REVERT: E  513 LEU cc_start: 0.9115 (mt) cc_final: 0.8802 (tt)
REVERT: L   49 TYR cc_start: 0.8237 (p90) cc_final: 0.7856 (p90)
  outliers start: 14
  outliers final: 13
  residues processed: 62
  average time/residue: 0.0429
  time to fit residues: 3.4923
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  : 0.105 
-------------------------------------------------------------------------------
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 0 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0070
   chunk 35 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.5398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.090736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.083023 restraints weight = 7333.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.084715 restraints weight = 4166.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.085930 restraints weight = 2679.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.086763 restraints weight = 1880.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.087405 restraints weight = 1433.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.5084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   2868  Z= 0.206
  Angle     :  0.662   7.074   3930  Z= 0.336
  Chirality :  0.045   0.138    440
  Planarity :  0.004   0.028    504
  Dihedral  :  5.475  32.298    482
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 24.66 %
    Favored  : 69.06 %
  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 aren not related in a simple way.
  whole: -0.69 (0.42), residues: 373
  helix: -2.47 (0.91), residues: 33
  sheet:  0.92 (0.46), residues: 119
  loop : -0.93 (0.39), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 457 
 TYR   0.010   0.001   TYR L  92 
 PHE   0.013   0.002   PHE E 374 
 TRP   0.019   0.002   TRP H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 2858)
  covalent geometry    : angle       0.65059 ( 3907)
  SS BOND              : bond        0.00618 (    7)
  SS BOND              : angle       1.60637 (   14)
  hydrogen bonds       : bond        0.03162 (  106)
  hydrogen bonds       : angle       6.04848 (  297)
  link_BETA1-4         : bond        0.00597 (    1)
  link_BETA1-4         : angle       2.22619 (    3)
  link_BETA1-6         : bond        0.00112 (    1)
  link_BETA1-6         : angle       1.86294 (    3)
  link_NAG-ASN         : bond        0.00186 (    1)
  link_NAG-ASN         : angle       1.34744 (    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
  69 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: H   48 MET cc_start: 0.7358 (ptp) cc_final: 0.6977 (mtm)
REVERT: H  118 GLN cc_start: 0.8069 (tp40) cc_final: 0.7846 (tp40)
REVERT: E  513 LEU cc_start: 0.9149 (mt) cc_final: 0.8759 (tt)
REVERT: L   49 TYR cc_start: 0.8278 (p90) cc_final: 0.8017 (p90)
  outliers start: 14
  outliers final: 13
  residues processed: 61
  average time/residue: 0.0427
  time to fit residues: 3.4373
Evaluate side-chains
  65 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  433 VAL
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  511 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0000
   chunk 35 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.5384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.090861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.082903 restraints weight = 7660.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.084664 restraints weight = 4301.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.085917 restraints weight = 2749.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.086826 restraints weight = 1928.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.087488 restraints weight = 1449.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.5237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   2868  Z= 0.208
  Angle     :  0.662   6.090   3930  Z= 0.338
  Chirality :  0.045   0.130    440
  Planarity :  0.005   0.031    504
  Dihedral  :  5.548  37.591    482
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 23.32 %
    Favored  : 69.96 %
  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 aren not related in a simple way.
  whole: -0.82 (0.42), residues: 373
  helix: -2.46 (0.89), residues: 33
  sheet:  0.83 (0.46), residues: 119
  loop : -1.04 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 466 
 TYR   0.010   0.001   TYR L  92 
 PHE   0.012   0.002   PHE E 392 
 TRP   0.015   0.002   TRP H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 2858)
  covalent geometry    : angle       0.65194 ( 3907)
  SS BOND              : bond        0.00621 (    7)
  SS BOND              : angle       1.37317 (   14)
  hydrogen bonds       : bond        0.03174 (  106)
  hydrogen bonds       : angle       6.04378 (  297)
  link_BETA1-4         : bond        0.00559 (    1)
  link_BETA1-4         : angle       2.18569 (    3)
  link_BETA1-6         : bond        0.00056 (    1)
  link_BETA1-6         : angle       1.83424 (    3)
  link_NAG-ASN         : bond        0.00096 (    1)
  link_NAG-ASN         : angle       1.74615 (    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
  68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 53
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: H  118 GLN cc_start: 0.8125 (tp40) cc_final: 0.7886 (tp40)
REVERT: E  513 LEU cc_start: 0.9148 (mt) cc_final: 0.8760 (tt)
REVERT: L   49 TYR cc_start: 0.8276 (p90) cc_final: 0.8035 (p90)
  outliers start: 15
  outliers final: 14
  residues processed: 62
  average time/residue: 0.0447
  time to fit residues: 3.6466
Evaluate side-chains
  65 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
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  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   32 TYR
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:    0.5980
   chunk 6 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0570
   chunk 11 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.4498

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.092640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.085517 restraints weight = 7501.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.087036 restraints weight = 4388.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.088152 restraints weight = 2898.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.088951 restraints weight = 2065.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.089482 restraints weight = 1561.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.5366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   2868  Z= 0.177
  Angle     :  0.643   6.084   3930  Z= 0.326
  Chirality :  0.045   0.129    440
  Planarity :  0.004   0.032    504
  Dihedral  :  5.365  39.072    482
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 24.66 %
    Favored  : 69.06 %
  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 aren not related in a simple way.
  whole: -0.99 (0.42), residues: 373
  helix: -3.30 (0.80), residues: 33
  sheet:  0.78 (0.46), residues: 119
  loop : -1.08 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 403 
 TYR   0.010   0.001   TYR H  95 
 PHE   0.012   0.002   PHE E 392 
 TRP   0.013   0.002   TRP H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 2858)
  covalent geometry    : angle       0.63546 ( 3907)
  SS BOND              : bond        0.00556 (    7)
  SS BOND              : angle       1.23166 (   14)
  hydrogen bonds       : bond        0.03010 (  106)
  hydrogen bonds       : angle       5.90864 (  297)
  link_BETA1-4         : bond        0.00534 (    1)
  link_BETA1-4         : angle       2.17615 (    3)
  link_BETA1-6         : bond        0.00084 (    1)
  link_BETA1-6         : angle       1.67585 (    3)
  link_NAG-ASN         : bond        0.00185 (    1)
  link_NAG-ASN         : angle       1.28555 (    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
  69 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: H  118 GLN cc_start: 0.8076 (tp40) cc_final: 0.7821 (tp-100)
REVERT: E  429 PHE cc_start: 0.8678 (t80) cc_final: 0.8059 (t80)
REVERT: E  513 LEU cc_start: 0.9126 (mt) cc_final: 0.8812 (tt)
REVERT: L   49 TYR cc_start: 0.8222 (p90) cc_final: 0.8015 (p90)
  outliers start: 14
  outliers final: 14
  residues processed: 64
  average time/residue: 0.0510
  time to fit residues: 4.0860
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  : 0.106 
-------------------------------------------------------------------------------
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  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   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:    0.0570
   chunk 1 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0470
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.3196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.093508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.086340 restraints weight = 7490.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.087858 restraints weight = 4383.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.088987 restraints weight = 2890.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.089786 restraints weight = 2054.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.090355 restraints weight = 1557.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.5436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   2868  Z= 0.142
  Angle     :  0.635   6.360   3930  Z= 0.319
  Chirality :  0.044   0.128    440
  Planarity :  0.004   0.030    504
  Dihedral  :  5.158  38.757    482
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 25.56 %
    Favored  : 68.61 %
  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 aren not related in a simple way.
  whole: -0.96 (0.42), residues: 373
  helix: -3.24 (0.81), residues: 33
  sheet:  0.79 (0.46), residues: 119
  loop : -1.05 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  98 
 TYR   0.012   0.001   TYR H  95 
 PHE   0.012   0.002   PHE E 392 
 TRP   0.013   0.002   TRP E 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 2858)
  covalent geometry    : angle       0.62708 ( 3907)
  SS BOND              : bond        0.00697 (    7)
  SS BOND              : angle       1.27361 (   14)
  hydrogen bonds       : bond        0.02848 (  106)
  hydrogen bonds       : angle       5.88430 (  297)
  link_BETA1-4         : bond        0.00452 (    1)
  link_BETA1-4         : angle       1.99490 (    3)
  link_BETA1-6         : bond        0.00134 (    1)
  link_BETA1-6         : angle       1.55145 (    3)
  link_NAG-ASN         : bond        0.00195 (    1)
  link_NAG-ASN         : angle       1.20046 (    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
  68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
REVERT: H   48 MET cc_start: 0.7084 (ptp) cc_final: 0.6807 (mtm)
REVERT: H  118 GLN cc_start: 0.8131 (tp40) cc_final: 0.7874 (tp-100)
REVERT: E  429 PHE cc_start: 0.8602 (t80) cc_final: 0.8032 (t80)
REVERT: E  513 LEU cc_start: 0.9162 (mt) cc_final: 0.8793 (tt)
REVERT: L   49 TYR cc_start: 0.8116 (p90) cc_final: 0.7845 (p90)
  outliers start: 13
  outliers final: 13
  residues processed: 63
  average time/residue: 0.0519
  time to fit residues: 4.1146
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   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  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   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:    0.0980
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0670
   overall best weight:    0.4718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.092686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.085649 restraints weight = 7323.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.087156 restraints weight = 4294.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.088248 restraints weight = 2840.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.088969 restraints weight = 2030.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.089564 restraints weight = 1571.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.5522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   2868  Z= 0.187
  Angle     :  0.669   7.638   3930  Z= 0.337
  Chirality :  0.045   0.128    440
  Planarity :  0.005   0.034    504
  Dihedral  :  5.410  40.346    482
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 24.22 %
    Favored  : 69.96 %
  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 aren not related in a simple way.
  whole: -1.05 (0.42), residues: 373
  helix: -3.37 (0.77), residues: 33
  sheet:  0.81 (0.46), residues: 119
  loop : -1.16 (0.39), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  98 
 TYR   0.014   0.001   TYR H  95 
 PHE   0.012   0.002   PHE E 392 
 TRP   0.012   0.001   TRP H  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 2858)
  covalent geometry    : angle       0.65996 ( 3907)
  SS BOND              : bond        0.00626 (    7)
  SS BOND              : angle       1.56791 (   14)
  hydrogen bonds       : bond        0.03161 (  106)
  hydrogen bonds       : angle       5.98334 (  297)
  link_BETA1-4         : bond        0.00542 (    1)
  link_BETA1-4         : angle       2.00007 (    3)
  link_BETA1-6         : bond        0.00032 (    1)
  link_BETA1-6         : angle       1.71114 (    3)
  link_NAG-ASN         : bond        0.00164 (    1)
  link_NAG-ASN         : angle       1.18282 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 752.30 seconds
wall clock time: 13 minutes 27.68 seconds (807.68 seconds total)