Starting phenix.real_space_refine
on Wed Sep 17 05:20:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lae_62925/09_2025/9lae_62925.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lae_62925/09_2025/9lae_62925.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lae_62925/09_2025/9lae_62925.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lae_62925/09_2025/9lae_62925.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lae_62925/09_2025/9lae_62925.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lae_62925/09_2025/9lae_62925.cif"
  }
  resolution = 3.46
  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=   0.014
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      28      5.16       5
     C    3168      2.51       5
     N     815      2.21       5
     O     989      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5000
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "G"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "L"
      Number of atoms: 788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 788
          Classifications: {'peptide': 104}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 918
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
    Chain: "B"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 831
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 913
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 5, 'TRANS': 113}
    Chain: "G"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.37, per 1000 atoms: 0.27
  Number of scatterers: 5000
  At special positions: 0
  Unit cell: (94.138, 80.134, 104.252, 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      28     16.00
     O     989      8.00
     N     815      7.00
     C    3168      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS G 336 " - pdb=" SG  CYS G 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 379 " - pdb=" SG  CYS G 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 391 " - pdb=" SG  CYS G 525 " distance=2.06
    Simple disulfide: pdb=" SG  CYS G 480 " - pdb=" SG  CYS G 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG G 601 " - " ASN G 343 "
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 218.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1172

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 13 sheets defined
      5.9% alpha, 35.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'G' and resid 364 through 370
      removed outlier: 4.357A  pdb=" N   LEU G 368 " --> pdb=" O   ASP G 364 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TYR G 369 " --> pdb=" O   TYR G 365 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 385 through 389
      removed outlier: 4.042A  pdb=" N   ASN G 388 " --> pdb=" O   THR G 385 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 405 through 410
      removed outlier: 4.274A  pdb=" N   ARG G 408 " --> pdb=" O   ASP G 405 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.771A  pdb=" N   THR H  31 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.850A  pdb=" N   ASP H  90 " --> pdb=" O   ARG H  87 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 3.845A  pdb=" N   TYR A  32 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.785A  pdb=" N   SER A  91 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 354 through 358
      removed outlier: 4.003A  pdb=" N   ASN G 394 " --> pdb=" O   GLU G 516 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.961A  pdb=" N   SER L   7 " --> pdb=" O   THR L  22 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   THR L  22 " --> pdb=" O   SER L   7 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 14
      removed outlier: 6.170A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 102 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LYS L 104 " --> pdb=" O   MET L  11 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ALA L  13 " --> pdb=" O   LYS L 104 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'L' and resid 52 through 53
      removed outlier: 6.568A  pdb=" N   TRP L  34 " --> pdb=" O   PHE L  46 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.552A  pdb=" N   VAL H   5 " --> pdb=" O   ALA H  23 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU H  18 " --> pdb=" O   LEU H  83 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.570A  pdb=" N   ALA H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.529A  pdb=" N   TYR H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 4 through 5
      removed outlier: 3.561A  pdb=" N   LYS B  24 " --> pdb=" O   THR B   5 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ASP B  70 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.611A  pdb=" N   VAL B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   TYR B  49 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 3 through 5
    Processing sheet with id=AB3, first strand: chain 'A' and resid 9 through 12
      removed outlier: 7.109A  pdb=" N   GLU A  10 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLY A  49 " --> pdb=" O   TRP A  36 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LYS A  38 " --> pdb=" O   TRP A  47 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   TRP A  47 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   THR A  40 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   LEU A  45 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 9 through 12
      removed outlier: 7.109A  pdb=" N   GLU A  10 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   TYR A 109 " --> pdb=" O   ARG A  98 " (cutoff:3.500A)

    153 hydrogen bonds defined for protein.
    366 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: 0.96

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.16 -     1.30: 804
        1.30 -     1.44: 1548
        1.44 -     1.58: 2735
        1.58 -     1.72: 0
        1.72 -     1.86: 40
  Bond restraints: 5127
  Sorted by residual:
  bond pdb=" C   PHE G 392 "
       pdb=" O   PHE G 392 "
    ideal  model  delta    sigma   weight residual
    1.234  1.161  0.073 1.25e-02 6.40e+03 3.39e+01
  bond pdb=" CA  PHE G 347 "
       pdb=" C   PHE G 347 "
    ideal  model  delta    sigma   weight residual
    1.528  1.452  0.076 1.45e-02 4.76e+03 2.75e+01
  bond pdb=" CA  PHE G 347 "
       pdb=" CB  PHE G 347 "
    ideal  model  delta    sigma   weight residual
    1.530  1.450  0.080 1.61e-02 3.86e+03 2.47e+01
  bond pdb=" CA  PHE G 392 "
       pdb=" C   PHE G 392 "
    ideal  model  delta    sigma   weight residual
    1.522  1.471  0.051 1.24e-02 6.50e+03 1.68e+01
  bond pdb=" C   PHE G 347 "
       pdb=" O   PHE G 347 "
    ideal  model  delta    sigma   weight residual
    1.235  1.184  0.051 1.38e-02 5.25e+03 1.37e+01
  ... (remaining 5122 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 6858
        2.31 -     4.63: 88
        4.63 -     6.94: 14
        6.94 -     9.25: 2
        9.25 -    11.56: 2
  Bond angle restraints: 6964
  Sorted by residual:
  angle pdb=" N   PHE G 392 "
        pdb=" CA  PHE G 392 "
        pdb=" C   PHE G 392 "
      ideal   model   delta    sigma   weight residual
     108.96   97.40   11.56 1.49e+00 4.50e-01 6.02e+01
  angle pdb=" N   VAL G 341 "
        pdb=" CA  VAL G 341 "
        pdb=" C   VAL G 341 "
      ideal   model   delta    sigma   weight residual
     113.71  108.51    5.20 9.50e-01 1.11e+00 2.99e+01
  angle pdb=" CA  PHE G 392 "
        pdb=" C   PHE G 392 "
        pdb=" N   THR G 393 "
      ideal   model   delta    sigma   weight residual
     115.38  122.62   -7.24 1.45e+00 4.76e-01 2.49e+01
  angle pdb=" N   VAL G 503 "
        pdb=" CA  VAL G 503 "
        pdb=" C   VAL G 503 "
      ideal   model   delta    sigma   weight residual
     112.98  107.06    5.92 1.25e+00 6.40e-01 2.25e+01
  angle pdb=" CA  PHE G 392 "
        pdb=" C   PHE G 392 "
        pdb=" O   PHE G 392 "
      ideal   model   delta    sigma   weight residual
     121.45  117.00    4.45 1.07e+00 8.73e-01 1.73e+01
  ... (remaining 6959 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 2717
       17.82 -    35.64: 243
       35.64 -    53.45: 43
       53.45 -    71.27: 6
       71.27 -    89.09: 4
  Dihedral angle restraints: 3013
    sinusoidal: 1154
      harmonic: 1859
  Sorted by residual:
  dihedral pdb=" CB  CYS G 480 "
           pdb=" SG  CYS G 480 "
           pdb=" SG  CYS G 488 "
           pdb=" CB  CYS G 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.34  -70.34     1      1.00e+01 1.00e-02 6.37e+01
  dihedral pdb=" CA  CYS G 361 "
           pdb=" C   CYS G 361 "
           pdb=" N   VAL G 362 "
           pdb=" CA  VAL G 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.62   27.38     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CB  CYS G 336 "
           pdb=" SG  CYS G 336 "
           pdb=" SG  CYS G 361 "
           pdb=" CB  CYS G 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.49  -38.49     1      1.00e+01 1.00e-02 2.09e+01
  ... (remaining 3010 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 510
       0.044 -    0.089: 181
       0.089 -    0.133: 51
       0.133 -    0.177: 7
       0.177 -    0.221: 1
  Chirality restraints: 750
  Sorted by residual:
  chirality pdb=" CA  PHE G 392 "
            pdb=" N   PHE G 392 "
            pdb=" C   PHE G 392 "
            pdb=" CB  PHE G 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  PHE G 347 "
            pdb=" N   PHE G 347 "
            pdb=" C   PHE G 347 "
            pdb=" CB  PHE G 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.08e-01
  chirality pdb=" CA  PRO G 463 "
            pdb=" N   PRO G 463 "
            pdb=" C   PRO G 463 "
            pdb=" CB  PRO G 463 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.84e-01
  ... (remaining 747 not shown)

  Planarity restraints: 889
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG G 346 "   -0.010 2.00e-02 2.50e+03   2.08e-02 4.31e+00
        pdb=" C   ARG G 346 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ARG G 346 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   PHE G 347 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  58 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO B  59 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B  59 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  59 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP G 389 "   -0.008 2.00e-02 2.50e+03   1.68e-02 2.82e+00
        pdb=" C   ASP G 389 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ASP G 389 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU G 390 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 886 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 121
        2.68 -     3.23: 4582
        3.23 -     3.79: 7182
        3.79 -     4.34: 10120
        4.34 -     4.90: 17729
  Nonbonded interactions: 39734
  Sorted by model distance:
  nonbonded pdb=" OG  SER G 477 "
            pdb=" OD1 ASP A  99 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" OG  SER G 477 "
            pdb=" O   TYR A 105 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   VAL L  25 "
            pdb=" OG1 THR L  68 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" N   PHE G 392 "
            pdb=" O   PHE G 392 "
     model   vdw
     2.234 2.496
  nonbonded pdb=" O   SER G 438 "
            pdb=" OG  SER G 438 "
     model   vdw
     2.248 3.040
  ... (remaining 39729 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=0.67 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             18.970
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.460
  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:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6824
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      :  0.006   0.080   5136  Z= 0.300
  Angle     :  0.746  11.563   6983  Z= 0.434
  Chirality :  0.048   0.221    750
  Planarity :  0.004   0.045    888
  Dihedral  : 13.670  89.090   1817
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.03 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -3.66 (0.28), residues: 635
  helix: -4.06 (0.70), residues: 26
  sheet: -1.75 (0.31), residues: 215
  loop : -2.84 (0.26), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  18 
 TYR   0.021   0.002   TYR G 505 
 PHE   0.021   0.002   PHE G 392 
 TRP   0.011   0.001   TRP G 436 
 HIS   0.002   0.001   HIS H  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 ( 5127)
  covalent geometry    : angle       0.72882 ( 6964)
  SS BOND              : bond        0.01013 (    8)
  SS BOND              : angle       2.33407 (   16)
  hydrogen bonds       : bond        0.16903 (  144)
  hydrogen bonds       : angle       7.35518 (  366)
  link_NAG-ASN         : bond        0.00725 (    1)
  link_NAG-ASN         : angle       5.86851 (    3)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G  346 ARG cc_start: 0.8146 (ttt180) cc_final: 0.7267 (ttm-80)
REVERT: G  408 ARG cc_start: 0.7815 (mtp180) cc_final: 0.7572 (mtm180)
REVERT: G  459 SER cc_start: 0.8141 (m) cc_final: 0.7781 (p)
REVERT: G  472 ILE cc_start: 0.6195 (mp) cc_final: 0.5869 (mm)
REVERT: L   51 SER cc_start: 0.8358 (t) cc_final: 0.8114 (p)
REVERT: H   31 THR cc_start: 0.8922 (t) cc_final: 0.8620 (p)
REVERT: H   63 SER cc_start: 0.8424 (m) cc_final: 0.8065 (p)
REVERT: H  108 MET cc_start: 0.8338 (mtt) cc_final: 0.8043 (mtt)
REVERT: H  113 GLN cc_start: 0.6904 (mt0) cc_final: 0.6108 (pt0)
REVERT: B   23 CYS cc_start: 0.5494 (t) cc_final: 0.4655 (t)
REVERT: B   37 GLN cc_start: 0.7868 (tt0) cc_final: 0.7666 (tt0)
REVERT: A   38 LYS cc_start: 0.6928 (tttt) cc_final: 0.6687 (tttm)
REVERT: A   80 TYR cc_start: 0.6538 (m-80) cc_final: 0.6192 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0876
  time to fit residues: 14.9690
Evaluate side-chains
  120 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0970
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    0.1980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
G 450 ASN
A   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.153290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.125520 restraints weight = 6511.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.17
r_work: 0.3244 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2954
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2954 r_free = 0.2954    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2952
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5136  Z= 0.141
  Angle     :  0.590   6.805   6983  Z= 0.312
  Chirality :  0.045   0.153    750
  Planarity :  0.004   0.047    888
  Dihedral  :  5.598  76.915    730
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 11.33 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -2.75 (0.30), residues: 635
  helix: -4.52 (0.65), residues: 20
  sheet: -1.00 (0.31), residues: 246
  loop : -2.33 (0.28), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 509 
 TYR   0.023   0.001   TYR G 369 
 PHE   0.018   0.001   PHE L  46 
 TRP   0.009   0.001   TRP G 436 
 HIS   0.001   0.001   HIS L  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5127)
  covalent geometry    : angle       0.57608 ( 6964)
  SS BOND              : bond        0.00551 (    8)
  SS BOND              : angle       1.85502 (   16)
  hydrogen bonds       : bond        0.03375 (  144)
  hydrogen bonds       : angle       5.76020 (  366)
  link_NAG-ASN         : bond        0.00283 (    1)
  link_NAG-ASN         : angle       4.55611 (    3)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.200 
Fit side-chains
REVERT: G  386 LYS cc_start: 0.8200 (mmpt) cc_final: 0.7950 (tttm)
REVERT: G  442 ASP cc_start: 0.8926 (m-30) cc_final: 0.8721 (m-30)
REVERT: G  472 ILE cc_start: 0.7865 (mp) cc_final: 0.7610 (mm)
REVERT: L    2 ILE cc_start: 0.8715 (mm) cc_final: 0.8501 (mm)
REVERT: H  113 GLN cc_start: 0.7607 (mt0) cc_final: 0.7189 (pt0)
REVERT: B   79 GLN cc_start: 0.7428 (mm-40) cc_final: 0.6846 (mt0)
REVERT: A   19 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7661 (ptmt)
REVERT: A   80 TYR cc_start: 0.7237 (m-80) cc_final: 0.6963 (m-80)
  outliers start: 13
  outliers final: 6
  residues processed: 132
  average time/residue: 0.0920
  time to fit residues: 15.1165
Evaluate side-chains
  120 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  345 THR
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   19 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 61 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
G 388 ASN
A  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.130418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.102087 restraints weight = 6865.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 2.12
r_work: 0.3117 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   5136  Z= 0.199
  Angle     :  0.618   9.269   6983  Z= 0.323
  Chirality :  0.045   0.146    750
  Planarity :  0.004   0.042    888
  Dihedral  :  5.454  67.165    730
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 14.63 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -2.48 (0.30), residues: 635
  helix: -4.32 (0.65), residues: 21
  sheet: -0.77 (0.31), residues: 248
  loop : -2.19 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 466 
 TYR   0.020   0.002   TYR G 369 
 PHE   0.010   0.001   PHE L  46 
 TRP   0.009   0.001   TRP L  90 
 HIS   0.002   0.001   HIS L  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 5127)
  covalent geometry    : angle       0.60052 ( 6964)
  SS BOND              : bond        0.00530 (    8)
  SS BOND              : angle       2.16548 (   16)
  hydrogen bonds       : bond        0.03650 (  144)
  hydrogen bonds       : angle       5.61459 (  366)
  link_NAG-ASN         : bond        0.00251 (    1)
  link_NAG-ASN         : angle       5.05956 (    3)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.204 
Fit side-chains
REVERT: G  386 LYS cc_start: 0.8244 (mmpt) cc_final: 0.7835 (tttm)
REVERT: G  442 ASP cc_start: 0.9092 (m-30) cc_final: 0.8841 (m-30)
REVERT: H  113 GLN cc_start: 0.7779 (mt0) cc_final: 0.7252 (pt0)
REVERT: B   79 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7270 (mm110)
REVERT: A   19 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7860 (ptmt)
REVERT: A   80 TYR cc_start: 0.7386 (m-80) cc_final: 0.6911 (m-80)
REVERT: A   85 SER cc_start: 0.7321 (m) cc_final: 0.7036 (t)
  outliers start: 17
  outliers final: 11
  residues processed: 124
  average time/residue: 0.0845
  time to fit residues: 13.2706
Evaluate side-chains
  121 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  345 THR
Chi-restraints excluded: chain G residue  361 CYS
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  517 LEU
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   28 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
G 388 ASN
B   8 GLN
A   3 GLN
A  82 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.129262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.100880 restraints weight = 6789.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.12
r_work: 0.3160 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3059
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3059
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   5136  Z= 0.226
  Angle     :  0.634  10.329   6983  Z= 0.330
  Chirality :  0.046   0.142    750
  Planarity :  0.004   0.042    888
  Dihedral  :  5.611  68.768    730
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 16.27 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -2.39 (0.30), residues: 635
  helix: -4.29 (0.66), residues: 21
  sheet: -0.66 (0.32), residues: 248
  loop : -2.16 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 466 
 TYR   0.019   0.002   TYR G 369 
 PHE   0.010   0.001   PHE L  46 
 TRP   0.009   0.001   TRP L  90 
 HIS   0.002   0.001   HIS L  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 ( 5127)
  covalent geometry    : angle       0.61669 ( 6964)
  SS BOND              : bond        0.00566 (    8)
  SS BOND              : angle       2.10648 (   16)
  hydrogen bonds       : bond        0.03640 (  144)
  hydrogen bonds       : angle       5.56353 (  366)
  link_NAG-ASN         : bond        0.00361 (    1)
  link_NAG-ASN         : angle       5.38809 (    3)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.212 
Fit side-chains
REVERT: G  442 ASP cc_start: 0.9095 (m-30) cc_final: 0.8887 (m-30)
REVERT: G  484 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7063 (tm-30)
REVERT: H  113 GLN cc_start: 0.7831 (mt0) cc_final: 0.7284 (pt0)
REVERT: B   79 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7311 (mm110)
REVERT: A   19 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7753 (ptmt)
REVERT: A   80 TYR cc_start: 0.7400 (m-80) cc_final: 0.6890 (m-80)
REVERT: A   85 SER cc_start: 0.7555 (m) cc_final: 0.7264 (t)
  outliers start: 26
  outliers final: 16
  residues processed: 131
  average time/residue: 0.0867
  time to fit residues: 14.3454
Evaluate side-chains
  127 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  345 THR
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  477 SER
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  517 LEU
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   72 LEU
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   96 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.4980
   chunk 9 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
A  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.130359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.102237 restraints weight = 6820.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.11
r_work: 0.3251 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2928
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2928
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   5136  Z= 0.159
  Angle     :  0.594   9.697   6983  Z= 0.308
  Chirality :  0.044   0.144    750
  Planarity :  0.004   0.044    888
  Dihedral  :  5.391  67.364    730
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 17.00 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -2.09 (0.31), residues: 635
  helix: -3.77 (0.78), residues: 20
  sheet: -0.40 (0.32), residues: 248
  loop : -2.04 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 466 
 TYR   0.017   0.001   TYR G 369 
 PHE   0.011   0.001   PHE L  46 
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 5127)
  covalent geometry    : angle       0.57837 ( 6964)
  SS BOND              : bond        0.00567 (    8)
  SS BOND              : angle       2.05221 (   16)
  hydrogen bonds       : bond        0.03333 (  144)
  hydrogen bonds       : angle       5.33434 (  366)
  link_NAG-ASN         : bond        0.00189 (    1)
  link_NAG-ASN         : angle       4.85001 (    3)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.209 
Fit side-chains
REVERT: H  113 GLN cc_start: 0.7773 (mt0) cc_final: 0.7322 (pt0)
REVERT: B   79 GLN cc_start: 0.7428 (mm-40) cc_final: 0.6929 (mt0)
REVERT: A   19 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7855 (ptmt)
REVERT: A   80 TYR cc_start: 0.7306 (m-80) cc_final: 0.7002 (m-80)
REVERT: A   85 SER cc_start: 0.7500 (m) cc_final: 0.7277 (t)
  outliers start: 24
  outliers final: 18
  residues processed: 129
  average time/residue: 0.0879
  time to fit residues: 14.2861
Evaluate side-chains
  128 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  333 THR
Chi-restraints excluded: chain G residue  345 THR
Chi-restraints excluded: chain G residue  389 ASP
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  477 SER
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  517 LEU
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   93 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 20 optimal weight:    6.9990
   chunk 5 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
A  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.130469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.102146 restraints weight = 6951.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 2.15
r_work: 0.3252 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2951
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2951
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   5136  Z= 0.166
  Angle     :  0.597   9.701   6983  Z= 0.308
  Chirality :  0.044   0.149    750
  Planarity :  0.004   0.044    888
  Dihedral  :  5.343  68.546    730
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 17.37 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -1.90 (0.31), residues: 635
  helix: -3.47 (0.88), residues: 21
  sheet: -0.22 (0.32), residues: 247
  loop : -1.94 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 466 
 TYR   0.018   0.001   TYR H  32 
 PHE   0.010   0.001   PHE L  46 
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 5127)
  covalent geometry    : angle       0.58031 ( 6964)
  SS BOND              : bond        0.00620 (    8)
  SS BOND              : angle       2.07861 (   16)
  hydrogen bonds       : bond        0.03318 (  144)
  hydrogen bonds       : angle       5.26584 (  366)
  link_NAG-ASN         : bond        0.00260 (    1)
  link_NAG-ASN         : angle       4.87774 (    3)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.245 
Fit side-chains
REVERT: H  113 GLN cc_start: 0.7805 (mt0) cc_final: 0.7323 (pt0)
REVERT: B   79 GLN cc_start: 0.7422 (mm-40) cc_final: 0.6953 (mt0)
REVERT: A   19 LYS cc_start: 0.8362 (ptmt) cc_final: 0.7659 (ptmt)
  outliers start: 26
  outliers final: 20
  residues processed: 135
  average time/residue: 0.0852
  time to fit residues: 14.5484
Evaluate side-chains
  129 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  333 THR
Chi-restraints excluded: chain G residue  345 THR
Chi-restraints excluded: chain G residue  389 ASP
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  477 SER
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  517 LEU
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   46 PHE
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   93 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 59 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0470
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.5680

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
A  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.131157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.103118 restraints weight = 6858.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.12
r_work: 0.3260 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   5136  Z= 0.159
  Angle     :  0.610  10.161   6983  Z= 0.314
  Chirality :  0.045   0.147    750
  Planarity :  0.004   0.039    888
  Dihedral  :  5.325  70.508    730
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 18.83 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -1.86 (0.31), residues: 635
  helix: -3.42 (0.88), residues: 21
  sheet: -0.31 (0.31), residues: 257
  loop : -1.86 (0.30), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  72 
 TYR   0.016   0.001   TYR H  32 
 PHE   0.010   0.001   PHE L  46 
 TRP   0.009   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 5127)
  covalent geometry    : angle       0.59411 ( 6964)
  SS BOND              : bond        0.00745 (    8)
  SS BOND              : angle       2.09818 (   16)
  hydrogen bonds       : bond        0.03294 (  144)
  hydrogen bonds       : angle       5.25772 (  366)
  link_NAG-ASN         : bond        0.00242 (    1)
  link_NAG-ASN         : angle       4.76618 (    3)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 0.186 
Fit side-chains
REVERT: H  113 GLN cc_start: 0.7788 (mt0) cc_final: 0.7321 (pt0)
REVERT: B   79 GLN cc_start: 0.7415 (mm-40) cc_final: 0.6960 (mt0)
REVERT: A   19 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8050 (mmtt)
  outliers start: 26
  outliers final: 17
  residues processed: 126
  average time/residue: 0.0760
  time to fit residues: 12.3531
Evaluate side-chains
  125 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  333 THR
Chi-restraints excluded: chain G residue  345 THR
Chi-restraints excluded: chain G residue  389 ASP
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  477 SER
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  517 LEU
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
A  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.131782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.102859 restraints weight = 6809.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.25
r_work: 0.3208 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   5136  Z= 0.209
  Angle     :  0.643  11.179   6983  Z= 0.331
  Chirality :  0.045   0.148    750
  Planarity :  0.004   0.039    888
  Dihedral  :  5.651  77.070    730
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 18.46 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -1.86 (0.31), residues: 635
  helix: -3.36 (0.89), residues: 21
  sheet: -0.22 (0.32), residues: 247
  loop : -1.90 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 466 
 TYR   0.015   0.002   TYR H  32 
 PHE   0.028   0.001   PHE L  46 
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 5127)
  covalent geometry    : angle       0.62380 ( 6964)
  SS BOND              : bond        0.00663 (    8)
  SS BOND              : angle       2.32602 (   16)
  hydrogen bonds       : bond        0.03515 (  144)
  hydrogen bonds       : angle       5.38378 (  366)
  link_NAG-ASN         : bond        0.00364 (    1)
  link_NAG-ASN         : angle       5.36165 (    3)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.207 
Fit side-chains
REVERT: H   84 SER cc_start: 0.9121 (p) cc_final: 0.8887 (t)
REVERT: H  113 GLN cc_start: 0.7946 (mt0) cc_final: 0.7325 (pt0)
REVERT: B   79 GLN cc_start: 0.7505 (mm-40) cc_final: 0.6903 (mt0)
REVERT: A   19 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7955 (mttt)
  outliers start: 28
  outliers final: 19
  residues processed: 127
  average time/residue: 0.0824
  time to fit residues: 13.3500
Evaluate side-chains
  126 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  333 THR
Chi-restraints excluded: chain G residue  345 THR
Chi-restraints excluded: chain G residue  389 ASP
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  477 SER
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  517 LEU
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   96 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 40 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 1 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0770
   chunk 29 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
G 487 ASN
B  89 GLN
A   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.152538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.124835 restraints weight = 6457.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.18
r_work: 0.3233 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2892
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2892
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   5136  Z= 0.156
  Angle     :  0.621  10.745   6983  Z= 0.318
  Chirality :  0.045   0.170    750
  Planarity :  0.004   0.041    888
  Dihedral  :  5.614  80.132    730
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 19.38 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -1.80 (0.31), residues: 635
  helix: -3.24 (0.92), residues: 21
  sheet: -0.28 (0.32), residues: 256
  loop : -1.81 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 403 
 TYR   0.016   0.001   TYR H  32 
 PHE   0.025   0.001   PHE L  46 
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 5127)
  covalent geometry    : angle       0.60773 ( 6964)
  SS BOND              : bond        0.00812 (    8)
  SS BOND              : angle       1.86282 (   16)
  hydrogen bonds       : bond        0.03283 (  144)
  hydrogen bonds       : angle       5.30156 (  366)
  link_NAG-ASN         : bond        0.00238 (    1)
  link_NAG-ASN         : angle       4.81152 (    3)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.192 
Fit side-chains
REVERT: L   64 SER cc_start: 0.8118 (t) cc_final: 0.7905 (p)
REVERT: L  102 GLU cc_start: 0.7384 (tt0) cc_final: 0.6911 (tp30)
REVERT: H  113 GLN cc_start: 0.7765 (mt0) cc_final: 0.7308 (pt0)
REVERT: B   79 GLN cc_start: 0.7418 (mm-40) cc_final: 0.6961 (mt0)
REVERT: A   19 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7858 (mttt)
  outliers start: 22
  outliers final: 14
  residues processed: 122
  average time/residue: 0.0828
  time to fit residues: 12.8543
Evaluate side-chains
  123 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  333 THR
Chi-restraints excluded: chain G residue  345 THR
Chi-restraints excluded: chain G residue  389 ASP
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  517 LEU
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    0.1980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
A   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.152389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.124552 restraints weight = 6536.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.19
r_work: 0.3225 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   5136  Z= 0.169
  Angle     :  0.636  11.179   6983  Z= 0.326
  Chirality :  0.045   0.176    750
  Planarity :  0.004   0.041    888
  Dihedral  :  5.701  84.277    730
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 20.66 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -1.83 (0.31), residues: 635
  helix: -3.26 (0.92), residues: 21
  sheet: -0.36 (0.32), residues: 246
  loop : -1.74 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 466 
 TYR   0.015   0.001   TYR H  32 
 PHE   0.026   0.001   PHE L  46 
 TRP   0.007   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 5127)
  covalent geometry    : angle       0.62150 ( 6964)
  SS BOND              : bond        0.00778 (    8)
  SS BOND              : angle       1.94196 (   16)
  hydrogen bonds       : bond        0.03319 (  144)
  hydrogen bonds       : angle       5.30014 (  366)
  link_NAG-ASN         : bond        0.00266 (    1)
  link_NAG-ASN         : angle       4.89161 (    3)

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

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

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1270 Ramachandran restraints generated.
    635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.174 
Fit side-chains
REVERT: L   64 SER cc_start: 0.8114 (t) cc_final: 0.7886 (p)
REVERT: L  102 GLU cc_start: 0.7378 (tt0) cc_final: 0.6894 (tp30)
REVERT: H  108 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8290 (mtt)
REVERT: H  113 GLN cc_start: 0.7775 (mt0) cc_final: 0.7321 (pt0)
REVERT: B   79 GLN cc_start: 0.7432 (mm-40) cc_final: 0.6962 (mt0)
REVERT: A   19 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7873 (mttm)
  outliers start: 18
  outliers final: 15
  residues processed: 114
  average time/residue: 0.0863
  time to fit residues: 12.3730
Evaluate side-chains
  121 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  333 THR
Chi-restraints excluded: chain G residue  345 THR
Chi-restraints excluded: chain G residue  389 ASP
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  503 VAL
Chi-restraints excluded: chain G residue  517 LEU
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain H residue  108 MET
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.130837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.102321 restraints weight = 6843.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.19
r_work: 0.3205 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2863
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.2863
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   5136  Z= 0.207
  Angle     :  0.659  11.164   6983  Z= 0.338
  Chirality :  0.046   0.180    750
  Planarity :  0.004   0.040    888
  Dihedral  :  5.914  87.904    730
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.29 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -1.81 (0.31), residues: 635
  helix: -3.32 (0.89), residues: 21
  sheet: -0.24 (0.32), residues: 236
  loop : -1.78 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 466 
 TYR   0.015   0.002   TYR H  32 
 PHE   0.030   0.002   PHE L  46 
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 5127)
  covalent geometry    : angle       0.64292 ( 6964)
  SS BOND              : bond        0.00766 (    8)
  SS BOND              : angle       2.05324 (   16)
  hydrogen bonds       : bond        0.03497 (  144)
  hydrogen bonds       : angle       5.39784 (  366)
  link_NAG-ASN         : bond        0.00348 (    1)
  link_NAG-ASN         : angle       5.32378 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1882.67 seconds
wall clock time: 33 minutes 5.77 seconds (1985.77 seconds total)