Starting phenix.real_space_refine
on Sat May 10 04:28:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lae_62925/05_2025/9lae_62925.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lae_62925/05_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_62925/05_2025/9lae_62925.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lae_62925/05_2025/9lae_62925.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lae_62925/05_2025/9lae_62925.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lae_62925/05_2025/9lae_62925.cif"
  }
  resolution = 3.46
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.00, per 1000 atoms: 1.40
  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: 1.14
  Conformation dependent library (CDL) restraints added in 575.2 milliseconds
  

  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: 0.71
  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: 1.43

  Time building geometry restraints manager: 1.35 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:             13.260
  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:          0.330
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     19.100
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.690
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.011   0.001   TRP G 436 
 HIS   0.002   0.001   HIS H  99 
 PHE   0.021   0.002   PHE G 392 
 TYR   0.021   0.002   TYR G 505 
 ARG   0.002   0.000   ARG B  18 

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

*********************** 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  : 0.560 
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: 0.7780 (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: 0.6088 (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: 0.7667 (tt0)
REVERT: A   38 LYS cc_start: 0.6928 (tttt) cc_final: 0.6695 (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: 0.1875
  time to fit residues: 31.9718
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  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:   20.0000
   chunk 46 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
G 388 ASN
G 450 ASN
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 = 0.3651 r_free = 0.3651 target = 0.147828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.119929 restraints weight = 6458.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.14
r_work: 0.3199 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2728
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2728 r_free = 0.2728    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.075   5136  Z= 0.281
  Angle     :  0.694  10.546   6983  Z= 0.366
  Chirality :  0.048   0.150    750
  Planarity :  0.005   0.046    888
  Dihedral  :  6.125  81.030    730
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.24 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 12.61 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.29), residues: 635
  helix: -4.52 (0.66), residues: 20
  sheet: -1.46 (0.31), residues: 234
  loop : -2.45 (0.27), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  33 
 PHE   0.016   0.002   PHE L  46 
 TYR   0.024   0.002   TYR G 369 
 ARG   0.002   0.000   ARG G 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00592 (    1)
  link_NAG-ASN         : angle       6.11726 (    3)
  hydrogen bonds       : bond        0.04181 (  144)
  hydrogen bonds       : angle       6.03973 (  366)
  SS BOND              : bond        0.00677 (    8)
  SS BOND              : angle       2.41841 (   16)
  covalent geometry    : bond        0.00677 ( 5127)
  covalent geometry    : angle       0.67366 ( 6964)

*********************** 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
  134 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.584 
Fit side-chains
REVERT: G  346 ARG cc_start: 0.8508 (ttt180) cc_final: 0.8052 (ttm-80)
REVERT: G  442 ASP cc_start: 0.9096 (m-30) cc_final: 0.8782 (m-30)
REVERT: G  459 SER cc_start: 0.8869 (m) cc_final: 0.8638 (p)
REVERT: G  484 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7044 (tm-30)
REVERT: H  113 GLN cc_start: 0.7848 (mt0) cc_final: 0.7238 (pt0)
REVERT: B   79 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7237 (mm110)
REVERT: A   19 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7966 (ptmt)
REVERT: A   80 TYR cc_start: 0.7369 (m-80) cc_final: 0.6907 (m-80)
  outliers start: 17
  outliers final: 10
  residues processed: 126
  average time/residue: 0.2121
  time to fit residues: 33.4579
Evaluate side-chains
  122 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  345 THR
Chi-restraints excluded: chain L residue    5 THR
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   64 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 10 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 38 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0060
   chunk 19 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0970
   chunk 21 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.3994

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.131788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.103508 restraints weight = 6774.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.13
r_work: 0.3129 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5136  Z= 0.127
  Angle     :  0.576   7.616   6983  Z= 0.303
  Chirality :  0.044   0.148    750
  Planarity :  0.004   0.049    888
  Dihedral  :  5.607  81.436    730
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 14.63 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.30), residues: 635
  helix: -4.27 (0.71), residues: 20
  sheet: -0.72 (0.31), residues: 246
  loop : -2.15 (0.28), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G 436 
 HIS   0.001   0.000   HIS L  88 
 PHE   0.025   0.001   PHE L  46 
 TYR   0.019   0.001   TYR G 369 
 ARG   0.001   0.000   ARG G 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00266 (    1)
  link_NAG-ASN         : angle       4.69853 (    3)
  hydrogen bonds       : bond        0.03327 (  144)
  hydrogen bonds       : angle       5.47397 (  366)
  SS BOND              : bond        0.00295 (    8)
  SS BOND              : angle       1.80598 (   16)
  covalent geometry    : bond        0.00309 ( 5127)
  covalent geometry    : angle       0.56194 ( 6964)

*********************** 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
  138 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.658 
Fit side-chains
REVERT: G  346 ARG cc_start: 0.8576 (ttt180) cc_final: 0.8090 (ttm-80)
REVERT: G  442 ASP cc_start: 0.9011 (m-30) cc_final: 0.8811 (m-30)
REVERT: H  113 GLN cc_start: 0.7771 (mt0) cc_final: 0.7220 (pt0)
REVERT: B   79 GLN cc_start: 0.7497 (mm-40) cc_final: 0.6908 (mt0)
REVERT: A   19 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7763 (ptmt)
REVERT: A   80 TYR cc_start: 0.7327 (m-80) cc_final: 0.7050 (m-80)
  outliers start: 20
  outliers final: 11
  residues processed: 133
  average time/residue: 0.1720
  time to fit residues: 29.2860
Evaluate side-chains
  120 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  361 CYS
Chi-restraints excluded: chain G residue  388 ASN
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   77 VAL
Chi-restraints excluded: chain H residue   69 THR
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
G 388 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 = 0.3454 r_free = 0.3454 target = 0.133944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.105831 restraints weight = 6752.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.10
r_work: 0.3209 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2870
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2870 r_free = 0.2870    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2870
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   5136  Z= 0.195
  Angle     :  0.613  10.083   6983  Z= 0.318
  Chirality :  0.045   0.146    750
  Planarity :  0.004   0.043    888
  Dihedral  :  5.827  86.555    730
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 16.45 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.31), residues: 635
  helix: -3.99 (0.73), residues: 21
  sheet: -0.55 (0.32), residues: 248
  loop : -2.05 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 
 PHE   0.031   0.002   PHE L  46 
 TYR   0.018   0.002   TYR G 369 
 ARG   0.001   0.000   ARG G 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00386 (    1)
  link_NAG-ASN         : angle       5.36836 (    3)
  hydrogen bonds       : bond        0.03493 (  144)
  hydrogen bonds       : angle       5.45452 (  366)
  SS BOND              : bond        0.00498 (    8)
  SS BOND              : angle       1.89189 (   16)
  covalent geometry    : bond        0.00474 ( 5127)
  covalent geometry    : angle       0.59696 ( 6964)

*********************** 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
  141 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.561 
Fit side-chains
REVERT: G  386 LYS cc_start: 0.8270 (mmpt) cc_final: 0.7957 (tttp)
REVERT: G  442 ASP cc_start: 0.8965 (m-30) cc_final: 0.8737 (m-30)
REVERT: H  113 GLN cc_start: 0.7729 (mt0) cc_final: 0.7269 (pt0)
REVERT: A   19 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7705 (ptmt)
REVERT: A   80 TYR cc_start: 0.7332 (m-80) cc_final: 0.7072 (m-80)
REVERT: A   85 SER cc_start: 0.7493 (m) cc_final: 0.7155 (t)
  outliers start: 25
  outliers final: 17
  residues processed: 136
  average time/residue: 0.1730
  time to fit residues: 29.9577
Evaluate side-chains
  132 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
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  361 CYS
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   72 LEU
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain H residue   40 THR
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 17 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
G 388 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 = 0.3396 r_free = 0.3396 target = 0.130220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.102021 restraints weight = 6790.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 2.18
r_work: 0.2865 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2710
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2710 r_free = 0.2710    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2710 r_free = 0.2710    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2710
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.1943

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= 0.196
  Angle     :  0.626  10.431   6983  Z= 0.324
  Chirality :  0.045   0.142    750
  Planarity :  0.004   0.044    888
  Dihedral  :  5.768  83.563    730
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 16.45 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.31), residues: 635
  helix: -4.07 (0.68), residues: 21
  sheet: -0.39 (0.32), residues: 248
  loop : -2.01 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 
 PHE   0.026   0.001   PHE L  46 
 TYR   0.015   0.001   TYR G 369 
 ARG   0.001   0.000   ARG G 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00392 (    1)
  link_NAG-ASN         : angle       5.46409 (    3)
  hydrogen bonds       : bond        0.03540 (  144)
  hydrogen bonds       : angle       5.41063 (  366)
  SS BOND              : bond        0.00404 (    8)
  SS BOND              : angle       1.99354 (   16)
  covalent geometry    : bond        0.00477 ( 5127)
  covalent geometry    : angle       0.60919 ( 6964)

*********************** 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
  138 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 0.562 
Fit side-chains
REVERT: G  442 ASP cc_start: 0.9139 (m-30) cc_final: 0.8900 (m-30)
REVERT: H  113 GLN cc_start: 0.7849 (mt0) cc_final: 0.7309 (pt0)
REVERT: A   19 LYS cc_start: 0.8492 (ptmt) cc_final: 0.7817 (ptmt)
REVERT: A   80 TYR cc_start: 0.7335 (m-80) cc_final: 0.6832 (m-80)
REVERT: A   85 SER cc_start: 0.7699 (m) cc_final: 0.7323 (t)
  outliers start: 27
  outliers final: 18
  residues processed: 130
  average time/residue: 0.1746
  time to fit residues: 28.9902
Evaluate side-chains
  128 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
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  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   72 LEU
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue   37 GLN
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   82 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    0.3980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  77 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 = 0.3377 r_free = 0.3377 target = 0.128862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.100191 restraints weight = 6773.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 2.18
r_work: 0.2899 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2743
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2743
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   5136  Z= 0.195
  Angle     :  0.627  10.908   6983  Z= 0.323
  Chirality :  0.045   0.146    750
  Planarity :  0.004   0.044    888
  Dihedral  :  5.889  89.703    730
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 16.09 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.31), residues: 635
  helix: -3.82 (0.74), residues: 21
  sheet: -0.34 (0.32), residues: 248
  loop : -1.97 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 
 PHE   0.024   0.001   PHE L  46 
 TYR   0.017   0.001   TYR A  27 
 ARG   0.001   0.000   ARG G 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00369 (    1)
  link_NAG-ASN         : angle       5.45963 (    3)
  hydrogen bonds       : bond        0.03485 (  144)
  hydrogen bonds       : angle       5.41480 (  366)
  SS BOND              : bond        0.00618 (    8)
  SS BOND              : angle       2.21175 (   16)
  covalent geometry    : bond        0.00475 ( 5127)
  covalent geometry    : angle       0.60873 ( 6964)

*********************** 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: 28
    poor density    : 116
  time to evaluate  : 0.621 
Fit side-chains
REVERT: G  442 ASP cc_start: 0.9109 (m-30) cc_final: 0.8858 (m-30)
REVERT: H   84 SER cc_start: 0.9070 (p) cc_final: 0.8819 (t)
REVERT: H  113 GLN cc_start: 0.7880 (mt0) cc_final: 0.7310 (pt0)
REVERT: A   19 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7858 (ptmt)
REVERT: A   85 SER cc_start: 0.7853 (m) cc_final: 0.7550 (t)
  outliers start: 28
  outliers final: 21
  residues processed: 136
  average time/residue: 0.1725
  time to fit residues: 30.3242
Evaluate side-chains
  130 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
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  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   72 LEU
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue   37 GLN
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   82 GLN
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue   96 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   chunk 55 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.5982

-------------------------------------------------------------------------------
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 = 0.3399 r_free = 0.3399 target = 0.130733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.102148 restraints weight = 6755.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.12
r_work: 0.2917 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2773 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2997
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2997 r_free = 0.2997    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   5136  Z= 0.168
  Angle     :  0.623  10.197   6983  Z= 0.321
  Chirality :  0.045   0.151    750
  Planarity :  0.004   0.045    888
  Dihedral  :  5.769  86.891    730
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 17.00 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.31), residues: 635
  helix: -3.60 (0.80), residues: 21
  sheet: -0.23 (0.32), residues: 247
  loop : -1.92 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 
 PHE   0.035   0.001   PHE L  46 
 TYR   0.012   0.001   TYR G 369 
 ARG   0.001   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00322 (    1)
  link_NAG-ASN         : angle       5.18706 (    3)
  hydrogen bonds       : bond        0.03323 (  144)
  hydrogen bonds       : angle       5.37506 (  366)
  SS BOND              : bond        0.00771 (    8)
  SS BOND              : angle       2.29962 (   16)
  covalent geometry    : bond        0.00414 ( 5127)
  covalent geometry    : angle       0.60404 ( 6964)

*********************** 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
  139 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.610 
Fit side-chains
REVERT: G  442 ASP cc_start: 0.9092 (m-30) cc_final: 0.8839 (m-30)
REVERT: H   84 SER cc_start: 0.9041 (p) cc_final: 0.8760 (t)
REVERT: H  113 GLN cc_start: 0.7836 (mt0) cc_final: 0.7264 (pt0)
REVERT: A   19 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7890 (mttt)
REVERT: A   85 SER cc_start: 0.7897 (m) cc_final: 0.7637 (t)
  outliers start: 26
  outliers final: 19
  residues processed: 130
  average time/residue: 0.1941
  time to fit residues: 32.1576
Evaluate side-chains
  128 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
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   72 LEU
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue   37 GLN
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   82 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 36 optimal weight:    0.4980
   chunk 34 optimal weight:    0.8980
   chunk 1 optimal weight:    0.3980
   chunk 5 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 59 optimal weight:    0.3980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.130784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.101849 restraints weight = 6825.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 2.20
r_work: 0.2924 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2808
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2808
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   5136  Z= 0.158
  Angle     :  0.608   9.878   6983  Z= 0.313
  Chirality :  0.044   0.148    750
  Planarity :  0.004   0.045    888
  Dihedral  :  5.612  82.981    730
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 17.55 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.31), residues: 635
  helix: -3.39 (0.88), residues: 21
  sheet: -0.15 (0.32), residues: 246
  loop : -1.86 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L  93 
 HIS   0.002   0.001   HIS L  88 
 PHE   0.029   0.001   PHE L  46 
 TYR   0.011   0.001   TYR G 453 
 ARG   0.002   0.000   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00301 (    1)
  link_NAG-ASN         : angle       4.85878 (    3)
  hydrogen bonds       : bond        0.03289 (  144)
  hydrogen bonds       : angle       5.31210 (  366)
  SS BOND              : bond        0.00662 (    8)
  SS BOND              : angle       2.26359 (   16)
  covalent geometry    : bond        0.00391 ( 5127)
  covalent geometry    : angle       0.59013 ( 6964)

*********************** 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
  134 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.548 
Fit side-chains
REVERT: G  442 ASP cc_start: 0.9080 (m-30) cc_final: 0.8833 (m-30)
REVERT: L   64 SER cc_start: 0.8150 (t) cc_final: 0.7819 (p)
REVERT: H  113 GLN cc_start: 0.7824 (mt0) cc_final: 0.7283 (pt0)
REVERT: A   19 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8165 (mmtt)
REVERT: A   85 SER cc_start: 0.7965 (m) cc_final: 0.7746 (t)
  outliers start: 26
  outliers final: 18
  residues processed: 124
  average time/residue: 0.1793
  time to fit residues: 28.1020
Evaluate side-chains
  125 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
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   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   37 GLN
Chi-restraints excluded: chain B residue   89 GLN
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3384 r_free = 0.3384 target = 0.129363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.100789 restraints weight = 6736.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 2.18
r_work: 0.3196 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3242 r_free = 0.3242    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   5136  Z= 0.201
  Angle     :  0.642  11.478   6983  Z= 0.331
  Chirality :  0.046   0.173    750
  Planarity :  0.005   0.045    888
  Dihedral  :  5.686  81.431    730
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 18.28 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.31), residues: 635
  helix: -3.43 (0.86), residues: 21
  sheet: -0.23 (0.32), residues: 248
  loop : -1.85 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 
 PHE   0.030   0.001   PHE L  46 
 TYR   0.013   0.001   TYR G 453 
 ARG   0.001   0.000   ARG H  38 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00367 (    1)
  link_NAG-ASN         : angle       5.24208 (    3)
  hydrogen bonds       : bond        0.03488 (  144)
  hydrogen bonds       : angle       5.38847 (  366)
  SS BOND              : bond        0.00916 (    8)
  SS BOND              : angle       2.16567 (   16)
  covalent geometry    : bond        0.00492 ( 5127)
  covalent geometry    : angle       0.62529 ( 6964)

*********************** 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
  132 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.513 
Fit side-chains
REVERT: G  442 ASP cc_start: 0.9001 (m-30) cc_final: 0.8781 (m-30)
REVERT: H   84 SER cc_start: 0.9033 (p) cc_final: 0.8798 (t)
REVERT: H  113 GLN cc_start: 0.7767 (mt0) cc_final: 0.7328 (pt0)
  outliers start: 25
  outliers final: 20
  residues processed: 122
  average time/residue: 0.1791
  time to fit residues: 27.7402
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  : 0.570 
-------------------------------------------------------------------------------
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   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue   37 GLN
Chi-restraints excluded: chain B residue   89 GLN
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.9188

-------------------------------------------------------------------------------
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 = 0.3375 r_free = 0.3375 target = 0.128702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.099863 restraints weight = 6813.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.21
r_work: 0.3158 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3265
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3265 r_free = 0.3265    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3265
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   5136  Z= 0.224
  Angle     :  0.661  11.579   6983  Z= 0.340
  Chirality :  0.046   0.183    750
  Planarity :  0.005   0.044    888
  Dihedral  :  5.778  80.467    730
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 19.20 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.31), residues: 635
  helix: -3.47 (0.83), residues: 21
  sheet: -0.27 (0.32), residues: 249
  loop : -1.84 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP G 436 
 HIS   0.002   0.001   HIS L  88 
 PHE   0.033   0.002   PHE L  46 
 TYR   0.014   0.001   TYR G 453 
 ARG   0.002   0.000   ARG G 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00397 (    1)
  link_NAG-ASN         : angle       5.51074 (    3)
  hydrogen bonds       : bond        0.03601 (  144)
  hydrogen bonds       : angle       5.45497 (  366)
  SS BOND              : bond        0.00770 (    8)
  SS BOND              : angle       2.26020 (   16)
  covalent geometry    : bond        0.00548 ( 5127)
  covalent geometry    : angle       0.64310 ( 6964)

********************** 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
  126 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.510 
Fit side-chains
REVERT: G  442 ASP cc_start: 0.9007 (m-30) cc_final: 0.8785 (m-30)
REVERT: H   84 SER cc_start: 0.9044 (p) cc_final: 0.8815 (t)
REVERT: H  113 GLN cc_start: 0.7790 (mt0) cc_final: 0.7344 (pt0)
  outliers start: 21
  outliers final: 18
  residues processed: 119
  average time/residue: 0.1732
  time to fit residues: 26.1029
Evaluate side-chains
  123 residues out of total 547 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
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   77 VAL
Chi-restraints excluded: chain L residue  103 ILE
Chi-restraints excluded: chain H residue   40 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  106 SER
Chi-restraints excluded: chain B residue   37 GLN
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain B residue  102 THR
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 55 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 0 optimal weight:    0.2980
   chunk 6 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 9 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0870
   chunk 47 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0980
   overall best weight:    0.2558

-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.134563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.105882 restraints weight = 6730.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 2.17
r_work: 0.2986 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5136  Z= 0.114
  Angle     :  0.591  10.581   6983  Z= 0.304
  Chirality :  0.044   0.163    750
  Planarity :  0.004   0.047    888
  Dihedral  :  5.336  79.644    730
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 20.48 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.32), residues: 635
  helix: -3.24 (0.94), residues: 20
  sheet: -0.12 (0.32), residues: 256
  loop : -1.65 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  93 
 HIS   0.001   0.000   HIS A  35 
 PHE   0.020   0.001   PHE L  46 
 TYR   0.013   0.001   TYR B  91 
 ARG   0.001   0.000   ARG G 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00105 (    1)
  link_NAG-ASN         : angle       4.12831 (    3)
  hydrogen bonds       : bond        0.03065 (  144)
  hydrogen bonds       : angle       5.19143 (  366)
  SS BOND              : bond        0.00777 (    8)
  SS BOND              : angle       1.77524 (   16)
  covalent geometry    : bond        0.00276 ( 5127)
  covalent geometry    : angle       0.57932 ( 6964)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3684.13 seconds
wall clock time: 66 minutes 3.26 seconds (3963.26 seconds total)