Starting phenix.real_space_refine
on Wed Jul 23 09:57:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r7n_24299/07_2025/7r7n_24299.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r7n_24299/07_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_24299/07_2025/7r7n_24299.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r7n_24299/07_2025/7r7n_24299.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r7n_24299/07_2025/7r7n_24299.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r7n_24299/07_2025/7r7n_24299.cif"
  }
  resolution = 3.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5}
          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, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          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: 3.87, per 1000 atoms: 1.39
  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: 0.95
  Conformation dependent library (CDL) restraints added in 540.2 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 10 sheets defined
      12.3% alpha, 38.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  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: 0.80

  Time building geometry restraints manager: 1.08 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:             4.080
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.070
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.260
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (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
 TRP   0.016   0.005   TRP L  35 
 PHE   0.016   0.003   PHE L  98 
 TYR   0.021   0.004   TYR L  92 
 ARG   0.003   0.000   ARG E 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05761 (    1)
  link_NAG-ASN         : angle       2.26738 (    3)
  link_BETA1-4         : bond        0.06871 (    1)
  link_BETA1-4         : angle       2.84603 (    3)
  hydrogen bonds       : bond        0.15942 (  106)
  hydrogen bonds       : angle       9.61620 (  297)
  link_BETA1-6         : bond        0.04724 (    1)
  link_BETA1-6         : angle       1.54020 (    3)
  SS BOND              : bond        0.07783 (    7)
  SS BOND              : angle       4.71542 (   14)
  covalent geometry    : bond        0.01027 ( 2858)
  covalent geometry    : angle       1.24490 ( 3907)

*********************** 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  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: H    3 GLN cc_start: 0.8454 (mp10) cc_final: 0.8035 (tp40)
REVERT: E  513 LEU cc_start: 0.8949 (mt) cc_final: 0.8631 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 100
  average time/residue: 0.1869
  time to fit residues: 21.4139
Evaluate side-chains
  56 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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 31 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 11 optimal weight:    0.3980
   chunk 17 optimal weight:    0.0770
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.3461 r_free = 0.3461 target = 0.098074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.090173 restraints weight = 7166.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.091939 restraints weight = 4207.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.093168 restraints weight = 2744.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.108   2868  Z= 0.213
  Angle     :  0.704   8.875   3930  Z= 0.365
  Chirality :  0.049   0.173    440
  Planarity :  0.004   0.036    504
  Dihedral  :  5.455  50.105    484
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 15.70 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.42), residues: 373
  helix: -3.46 (0.79), residues: 26
  sheet:  0.87 (0.48), residues: 119
  loop :  0.02 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  47 
 PHE   0.016   0.002   PHE H  29 
 TYR   0.019   0.002   TYR H  95 
 ARG   0.005   0.001   ARG E 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00084 (    1)
  link_NAG-ASN         : angle       1.78288 (    3)
  link_BETA1-4         : bond        0.00838 (    1)
  link_BETA1-4         : angle       1.61924 (    3)
  hydrogen bonds       : bond        0.03708 (  106)
  hydrogen bonds       : angle       6.81070 (  297)
  link_BETA1-6         : bond        0.00071 (    1)
  link_BETA1-6         : angle       2.17189 (    3)
  SS BOND              : bond        0.00684 (    7)
  SS BOND              : angle       1.88112 (   14)
  covalent geometry    : bond        0.00507 ( 2858)
  covalent geometry    : angle       0.69091 ( 3907)

*********************** 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
  77 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.339 
Fit side-chains
REVERT: H    3 GLN cc_start: 0.8262 (mp10) cc_final: 0.7993 (tp40)
REVERT: E  513 LEU cc_start: 0.9087 (mt) cc_final: 0.8814 (tt)
REVERT: L   49 TYR cc_start: 0.8052 (p90) cc_final: 0.7445 (p90)
REVERT: L   96 ARG cc_start: 0.7219 (ttt-90) cc_final: 0.6890 (ttm170)
  outliers start: 15
  outliers final: 10
  residues processed: 70
  average time/residue: 0.1303
  time to fit residues: 11.2233
Evaluate side-chains
  58 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  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   20 THR
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:    0.8980
   chunk 20 optimal weight:    0.0070
   chunk 29 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 28 optimal weight:    0.4980
   chunk 4 optimal weight:    0.4980
   chunk 30 optimal weight:    0.0980
   chunk 34 optimal weight:    0.6980
   chunk 16 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9990
   chunk 18 optimal weight:    0.4980
   overall best weight:    0.2998

-------------------------------------------------------------------------------
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 = 0.3453 r_free = 0.3453 target = 0.097577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.089437 restraints weight = 7144.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.091284 restraints weight = 4078.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.092648 restraints weight = 2639.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   2868  Z= 0.143
  Angle     :  0.594   6.076   3930  Z= 0.308
  Chirality :  0.044   0.136    440
  Planarity :  0.004   0.031    504
  Dihedral  :  4.953  43.903    484
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 19.73 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.43), residues: 373
  helix: -2.97 (0.93), residues: 26
  sheet:  0.64 (0.45), residues: 129
  loop : -0.03 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 PHE   0.029   0.002   PHE E 374 
 TYR   0.013   0.001   TYR E 423 
 ARG   0.004   0.000   ARG E 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00287 (    1)
  link_NAG-ASN         : angle       1.48187 (    3)
  link_BETA1-4         : bond        0.00440 (    1)
  link_BETA1-4         : angle       1.80931 (    3)
  hydrogen bonds       : bond        0.03284 (  106)
  hydrogen bonds       : angle       6.39134 (  297)
  link_BETA1-6         : bond        0.00214 (    1)
  link_BETA1-6         : angle       1.56733 (    3)
  SS BOND              : bond        0.00875 (    7)
  SS BOND              : angle       1.27193 (   14)
  covalent geometry    : bond        0.00328 ( 2858)
  covalent geometry    : angle       0.58531 ( 3907)

*********************** 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
  70 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 0.330 
Fit side-chains
REVERT: H    3 GLN cc_start: 0.8248 (mp10) cc_final: 0.7977 (tp40)
REVERT: E  513 LEU cc_start: 0.9058 (mt) cc_final: 0.8713 (tt)
REVERT: L   49 TYR cc_start: 0.8067 (p90) cc_final: 0.7569 (p90)
  outliers start: 14
  outliers final: 11
  residues processed: 64
  average time/residue: 0.1077
  time to fit residues: 8.8614
Evaluate side-chains
  63 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  103 CYS
Chi-restraints excluded: chain H residue  108 CYS
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  392 PHE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  517 LEU
Chi-restraints excluded: chain L residue   88 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3326 r_free = 0.3326 target = 0.090140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.082802 restraints weight = 7369.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.084426 restraints weight = 4265.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.085638 restraints weight = 2775.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.4378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.115   2868  Z= 0.325
  Angle     :  0.749   6.938   3930  Z= 0.394
  Chirality :  0.048   0.158    440
  Planarity :  0.006   0.064    504
  Dihedral  :  6.461  45.172    484
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 21.52 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.42), residues: 373
  helix: -2.80 (1.01), residues: 26
  sheet:  0.94 (0.47), residues: 121
  loop : -0.71 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H  47 
 PHE   0.023   0.003   PHE E 374 
 TYR   0.016   0.002   TYR H  95 
 ARG   0.003   0.001   ARG E 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00026 (    1)
  link_NAG-ASN         : angle       2.28677 (    3)
  link_BETA1-4         : bond        0.00907 (    1)
  link_BETA1-4         : angle       2.35093 (    3)
  hydrogen bonds       : bond        0.03932 (  106)
  hydrogen bonds       : angle       6.36837 (  297)
  link_BETA1-6         : bond        0.00227 (    1)
  link_BETA1-6         : angle       2.48744 (    3)
  SS BOND              : bond        0.00980 (    7)
  SS BOND              : angle       1.65503 (   14)
  covalent geometry    : bond        0.00740 ( 2858)
  covalent geometry    : angle       0.73625 ( 3907)

*********************** 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
  68 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: H    3 GLN cc_start: 0.8336 (mp10) cc_final: 0.8084 (tp40)
REVERT: E  442 ASP cc_start: 0.8879 (t0) cc_final: 0.8652 (t0)
REVERT: E  513 LEU cc_start: 0.9179 (mt) cc_final: 0.8825 (tt)
REVERT: L   49 TYR cc_start: 0.8246 (p90) cc_final: 0.7825 (p90)
  outliers start: 13
  outliers final: 13
  residues processed: 64
  average time/residue: 0.1102
  time to fit residues: 9.1503
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  : 0.254 
-------------------------------------------------------------------------------
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  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 14 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0070
   chunk 30 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 13 optimal weight:    0.4980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.4998

-------------------------------------------------------------------------------
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
L  34 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.092504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.085370 restraints weight = 7268.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.087008 restraints weight = 4194.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.088165 restraints weight = 2708.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.4603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   2868  Z= 0.192
  Angle     :  0.640   6.272   3930  Z= 0.329
  Chirality :  0.046   0.138    440
  Planarity :  0.004   0.034    504
  Dihedral  :  5.772  44.114    484
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 23.77 %
    Favored  : 69.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.43), residues: 373
  helix: -2.59 (1.04), residues: 26
  sheet:  1.02 (0.48), residues: 120
  loop : -0.84 (0.39), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  47 
 PHE   0.022   0.002   PHE H  29 
 TYR   0.010   0.001   TYR E 423 
 ARG   0.003   0.000   ARG L  96 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00222 (    1)
  link_NAG-ASN         : angle       1.58005 (    3)
  link_BETA1-4         : bond        0.00562 (    1)
  link_BETA1-4         : angle       2.43443 (    3)
  hydrogen bonds       : bond        0.03294 (  106)
  hydrogen bonds       : angle       6.19319 (  297)
  link_BETA1-6         : bond        0.00202 (    1)
  link_BETA1-6         : angle       1.95722 (    3)
  SS BOND              : bond        0.00629 (    7)
  SS BOND              : angle       1.23344 (   14)
  covalent geometry    : bond        0.00449 ( 2858)
  covalent geometry    : angle       0.63058 ( 3907)

*********************** 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
  69 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: H    3 GLN cc_start: 0.8399 (mp10) cc_final: 0.8056 (tp40)
REVERT: E  442 ASP cc_start: 0.8825 (t0) cc_final: 0.8592 (t0)
REVERT: E  513 LEU cc_start: 0.9168 (mt) cc_final: 0.8841 (tt)
REVERT: L   49 TYR cc_start: 0.8232 (p90) cc_final: 0.7815 (p90)
  outliers start: 15
  outliers final: 14
  residues processed: 62
  average time/residue: 0.1134
  time to fit residues: 8.9965
Evaluate side-chains
  66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  103 CYS
Chi-restraints excluded: chain H residue  108 CYS
Chi-restraints excluded: chain H residue  109 TYR
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  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 11 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 15 optimal weight:    0.1980
   chunk 14 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0020
   chunk 33 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0470
   chunk 8 optimal weight:    0.0980
   overall best weight:    0.2086

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

Flipped N/Q/H residues before XYZ refinement:
H 118 GLN
L  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.094917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.087510 restraints weight = 7182.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.089231 restraints weight = 4100.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.090442 restraints weight = 2623.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.4754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2868  Z= 0.117
  Angle     :  0.606   7.823   3930  Z= 0.305
  Chirality :  0.045   0.147    440
  Planarity :  0.004   0.042    504
  Dihedral  :  5.198  38.916    484
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 25.11 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.43), residues: 373
  helix: -2.37 (0.96), residues: 33
  sheet:  1.07 (0.48), residues: 118
  loop : -0.86 (0.40), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  47 
 PHE   0.015   0.002   PHE E 374 
 TYR   0.009   0.001   TYR H  95 
 ARG   0.003   0.000   ARG E 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00296 (    1)
  link_NAG-ASN         : angle       1.25643 (    3)
  link_BETA1-4         : bond        0.00353 (    1)
  link_BETA1-4         : angle       2.00064 (    3)
  hydrogen bonds       : bond        0.02850 (  106)
  hydrogen bonds       : angle       5.88917 (  297)
  link_BETA1-6         : bond        0.00235 (    1)
  link_BETA1-6         : angle       1.53784 (    3)
  SS BOND              : bond        0.00478 (    7)
  SS BOND              : angle       1.45633 (   14)
  covalent geometry    : bond        0.00268 ( 2858)
  covalent geometry    : angle       0.59635 ( 3907)

*********************** 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: 11
    poor density    : 58
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.8062 (t80) cc_final: 0.7816 (t80)
REVERT: E  442 ASP cc_start: 0.8822 (t0) cc_final: 0.8621 (t0)
REVERT: E  467 ASP cc_start: 0.7265 (t0) cc_final: 0.6983 (p0)
REVERT: E  513 LEU cc_start: 0.9130 (mt) cc_final: 0.8799 (tt)
REVERT: L   49 TYR cc_start: 0.8116 (p90) cc_final: 0.7713 (p90)
  outliers start: 11
  outliers final: 9
  residues processed: 65
  average time/residue: 0.1175
  time to fit residues: 9.6426
Evaluate side-chains
  59 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  103 CYS
Chi-restraints excluded: chain H residue  108 CYS
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  392 PHE
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  517 LEU
Chi-restraints excluded: chain L residue   88 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 32 optimal weight:    0.4980
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** L  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.090088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.082994 restraints weight = 7664.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.084623 restraints weight = 4326.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.085708 restraints weight = 2763.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.5197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.110   2868  Z= 0.291
  Angle     :  0.732   6.129   3930  Z= 0.380
  Chirality :  0.047   0.162    440
  Planarity :  0.005   0.031    504
  Dihedral  :  5.897  37.064    482
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.43), residues: 373
  helix: -2.25 (1.11), residues: 26
  sheet:  1.00 (0.47), residues: 120
  loop : -1.12 (0.39), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP H  47 
 PHE   0.014   0.002   PHE E 429 
 TYR   0.011   0.002   TYR L  92 
 ARG   0.007   0.001   ARG L  96 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00038 (    1)
  link_NAG-ASN         : angle       1.90242 (    3)
  link_BETA1-4         : bond        0.00876 (    1)
  link_BETA1-4         : angle       2.20351 (    3)
  hydrogen bonds       : bond        0.03656 (  106)
  hydrogen bonds       : angle       6.25018 (  297)
  link_BETA1-6         : bond        0.00112 (    1)
  link_BETA1-6         : angle       2.11321 (    3)
  SS BOND              : bond        0.00689 (    7)
  SS BOND              : angle       1.72206 (   14)
  covalent geometry    : bond        0.00679 ( 2858)
  covalent geometry    : angle       0.72019 ( 3907)

*********************** 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
  66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.8249 (t80) cc_final: 0.7847 (t80)
REVERT: E  442 ASP cc_start: 0.8880 (t0) cc_final: 0.8667 (t0)
REVERT: E  513 LEU cc_start: 0.9150 (mt) cc_final: 0.8896 (tt)
REVERT: L   49 TYR cc_start: 0.8273 (p90) cc_final: 0.7936 (p90)
  outliers start: 14
  outliers final: 14
  residues processed: 61
  average time/residue: 0.1191
  time to fit residues: 9.4269
Evaluate side-chains
  64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
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   47 LEU
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 15 optimal weight:    0.0060
   chunk 6 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    0.1980
   overall best weight:    0.3194

-------------------------------------------------------------------------------
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 = 0.3390 r_free = 0.3390 target = 0.093243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.085674 restraints weight = 7401.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.087464 restraints weight = 4085.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.088646 restraints weight = 2568.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.5245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   2868  Z= 0.148
  Angle     :  0.639   6.385   3930  Z= 0.325
  Chirality :  0.046   0.181    440
  Planarity :  0.004   0.029    504
  Dihedral  :  5.183  35.378    482
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 25.11 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.43), residues: 373
  helix: -2.43 (0.83), residues: 39
  sheet:  0.94 (0.46), residues: 120
  loop : -0.95 (0.41), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  47 
 PHE   0.014   0.002   PHE E 374 
 TYR   0.009   0.001   TYR L  49 
 ARG   0.005   0.000   ARG L  96 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00182 (    1)
  link_NAG-ASN         : angle       1.23455 (    3)
  link_BETA1-4         : bond        0.00418 (    1)
  link_BETA1-4         : angle       2.17674 (    3)
  hydrogen bonds       : bond        0.02999 (  106)
  hydrogen bonds       : angle       6.03627 (  297)
  link_BETA1-6         : bond        0.00185 (    1)
  link_BETA1-6         : angle       1.68274 (    3)
  SS BOND              : bond        0.00586 (    7)
  SS BOND              : angle       1.24068 (   14)
  covalent geometry    : bond        0.00353 ( 2858)
  covalent geometry    : angle       0.63089 ( 3907)

*********************** 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: 13
    poor density    : 55
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.8273 (t80) cc_final: 0.7887 (t80)
REVERT: E  513 LEU cc_start: 0.9156 (mt) cc_final: 0.8841 (tt)
REVERT: L   49 TYR cc_start: 0.8211 (p90) cc_final: 0.7901 (p90)
  outliers start: 13
  outliers final: 13
  residues processed: 63
  average time/residue: 0.1306
  time to fit residues: 10.1537
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  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  103 CYS
Chi-restraints excluded: chain H residue  108 CYS
Chi-restraints excluded: chain 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
Chi-restraints excluded: chain L residue   97 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 2 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 1 optimal weight:    0.3980
   chunk 10 optimal weight:    0.1980
   chunk 24 optimal weight:    0.0070
   chunk 32 optimal weight:    0.0070
   chunk 25 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.2016

-------------------------------------------------------------------------------
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 = 0.3415 r_free = 0.3415 target = 0.094495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.087238 restraints weight = 7377.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.088919 restraints weight = 4217.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.090101 restraints weight = 2709.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.5341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   2868  Z= 0.123
  Angle     :  0.631   6.447   3930  Z= 0.318
  Chirality :  0.045   0.151    440
  Planarity :  0.004   0.035    504
  Dihedral  :  4.889  35.198    482
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 26.01 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.43), residues: 373
  helix: -3.18 (0.83), residues: 33
  sheet:  0.89 (0.46), residues: 120
  loop : -0.90 (0.41), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  47 
 PHE   0.012   0.002   PHE E 392 
 TYR   0.014   0.001   TYR H  95 
 ARG   0.004   0.000   ARG L  96 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00220 (    1)
  link_NAG-ASN         : angle       1.01094 (    3)
  link_BETA1-4         : bond        0.00315 (    1)
  link_BETA1-4         : angle       1.84788 (    3)
  hydrogen bonds       : bond        0.02775 (  106)
  hydrogen bonds       : angle       5.88669 (  297)
  link_BETA1-6         : bond        0.00302 (    1)
  link_BETA1-6         : angle       1.57728 (    3)
  SS BOND              : bond        0.00518 (    7)
  SS BOND              : angle       1.43146 (   14)
  covalent geometry    : bond        0.00295 ( 2858)
  covalent geometry    : angle       0.62303 ( 3907)

*********************** 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: 13
    poor density    : 56
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: E  386 LYS cc_start: 0.9271 (mmtm) cc_final: 0.7559 (pttt)
REVERT: E  513 LEU cc_start: 0.9165 (mt) cc_final: 0.8806 (tt)
REVERT: L   49 TYR cc_start: 0.8117 (p90) cc_final: 0.7848 (p90)
  outliers start: 13
  outliers final: 13
  residues processed: 63
  average time/residue: 0.1282
  time to fit residues: 10.0228
Evaluate side-chains
  66 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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  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  468 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
Chi-restraints excluded: chain L residue   97 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 27 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0060
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.4396

-------------------------------------------------------------------------------
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 = 0.3385 r_free = 0.3385 target = 0.093037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.085793 restraints weight = 7427.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.087410 restraints weight = 4238.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.088602 restraints weight = 2758.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.5467

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= 0.182
  Angle     :  0.667   7.313   3930  Z= 0.339
  Chirality :  0.046   0.136    440
  Planarity :  0.004   0.029    504
  Dihedral  :  5.266  38.393    482
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 25.56 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.53 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.42), residues: 373
  helix: -3.25 (0.81), residues: 33
  sheet:  0.82 (0.47), residues: 114
  loop : -0.91 (0.40), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  47 
 PHE   0.016   0.002   PHE H  29 
 TYR   0.014   0.001   TYR H  95 
 ARG   0.005   0.001   ARG L  96 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00153 (    1)
  link_NAG-ASN         : angle       1.16402 (    3)
  link_BETA1-4         : bond        0.00573 (    1)
  link_BETA1-4         : angle       1.85909 (    3)
  hydrogen bonds       : bond        0.03209 (  106)
  hydrogen bonds       : angle       5.95806 (  297)
  link_BETA1-6         : bond        0.00119 (    1)
  link_BETA1-6         : angle       1.73139 (    3)
  SS BOND              : bond        0.00609 (    7)
  SS BOND              : angle       1.48070 (   14)
  covalent geometry    : bond        0.00437 ( 2858)
  covalent geometry    : angle       0.65890 ( 3907)

********************** 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
  65 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: H   29 PHE cc_start: 0.8151 (t80) cc_final: 0.7633 (t80)
REVERT: E  513 LEU cc_start: 0.9187 (mt) cc_final: 0.8807 (tt)
REVERT: L   49 TYR cc_start: 0.8200 (p90) cc_final: 0.7973 (p90)
  outliers start: 14
  outliers final: 14
  residues processed: 59
  average time/residue: 0.1119
  time to fit residues: 8.4672
Evaluate side-chains
  64 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
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  468 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
Chi-restraints excluded: chain L residue   97 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0870
   chunk 10 optimal weight:    0.0870
   chunk 35 optimal weight:    0.5980
   chunk 15 optimal weight:    0.1980
   chunk 31 optimal weight:    0.0040
   chunk 28 optimal weight:    0.3980
   chunk 12 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.1548

-------------------------------------------------------------------------------
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 = 0.3436 r_free = 0.3436 target = 0.095904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.088591 restraints weight = 7211.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.090255 restraints weight = 4140.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.091474 restraints weight = 2674.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.5519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2868  Z= 0.106
  Angle     :  0.627   7.133   3930  Z= 0.312
  Chirality :  0.045   0.134    440
  Planarity :  0.004   0.028    504
  Dihedral  :  4.653  34.583    482
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 25.11 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.43), residues: 373
  helix: -3.24 (0.79), residues: 33
  sheet:  0.97 (0.47), residues: 114
  loop : -0.76 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 436 
 PHE   0.013   0.002   PHE E 392 
 TYR   0.008   0.001   TYR E 423 
 ARG   0.002   0.000   ARG E 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00241 (    1)
  link_NAG-ASN         : angle       0.66850 (    3)
  link_BETA1-4         : bond        0.00306 (    1)
  link_BETA1-4         : angle       1.77441 (    3)
  hydrogen bonds       : bond        0.02652 (  106)
  hydrogen bonds       : angle       5.69924 (  297)
  link_BETA1-6         : bond        0.00266 (    1)
  link_BETA1-6         : angle       1.35544 (    3)
  SS BOND              : bond        0.00526 (    7)
  SS BOND              : angle       1.30804 (   14)
  covalent geometry    : bond        0.00252 ( 2858)
  covalent geometry    : angle       0.62060 ( 3907)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1490.49 seconds
wall clock time: 26 minutes 19.57 seconds (1579.57 seconds total)