Starting phenix.real_space_refine
on Thu Jul 24 05:26:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d8q_27254/07_2025/8d8q_27254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d8q_27254/07_2025/8d8q_27254.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d8q_27254/07_2025/8d8q_27254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d8q_27254/07_2025/8d8q_27254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d8q_27254/07_2025/8d8q_27254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d8q_27254/07_2025/8d8q_27254.cif"
  }
  resolution = 4.2
  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=   0.044
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      27      5.16       5
     C    3291      2.51       5
     N     874      2.21       5
     O    1010      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5202
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "H"
      Number of atoms: 996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 996
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 5, 'TRANS': 124}
    Chain: "L"
      Number of atoms: 883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 883
          Classifications: {'peptide': 114}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108}
    Chain: "A"
      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: "B"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 832
          Classifications: {'peptide': 109}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102}
    Chain: "C"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 941
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "A"
      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: 6.30, per 1000 atoms: 1.21
  Number of scatterers: 5202
  At special positions: 0
  Unit cell: (77.996, 94.86, 102.238, 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      27     16.00
     O    1010      8.00
     N     874      7.00
     C    3291      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.12
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.12
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  97 " - pdb=" SG  CYS C 102 " distance=2.05

  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 A1301 " - " ASN A 343 "
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 694.3 milliseconds
  

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1210

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 15 sheets defined
      11.4% alpha, 36.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'L' and resid 30B through 30F
      removed outlier: 4.153A  pdb=" N   LYS L  30F" --> pdb=" O   SER L  30C" (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 385 through 390
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.089A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'B' and resid 30 through 31
      No H-bonds generated for 'chain 'B' and resid 30 through 31'
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.540A  pdb=" N   PHE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 64
    Processing helix  chain 'C' and resid 83 through 87
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.826A  pdb=" N   MET H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   ARG H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.707A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.587A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.544A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AB1, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.551A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.551A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR B  97 " --> pdb=" O   HIS B  90 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.116A  pdb=" N   ARG C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   TRP C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12

    205 hydrogen bonds defined for protein.
    456 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: 1.66

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1000
        1.32 -     1.45: 1457
        1.45 -     1.57: 2834
        1.57 -     1.70: 0
        1.70 -     1.82: 36
  Bond restraints: 5327
  Sorted by residual:
  bond pdb=" CB  TYR L  91 "
       pdb=" CG  TYR L  91 "
    ideal  model  delta    sigma   weight residual
    1.512  1.449  0.063 2.20e-02 2.07e+03 8.16e+00
  bond pdb=" CG  ASP H  58 "
       pdb=" OD1 ASP H  58 "
    ideal  model  delta    sigma   weight residual
    1.249  1.198  0.051 1.90e-02 2.77e+03 7.25e+00
  bond pdb=" CB  ASN A 422 "
       pdb=" CG  ASN A 422 "
    ideal  model  delta    sigma   weight residual
    1.516  1.450  0.066 2.50e-02 1.60e+03 7.04e+00
  bond pdb=" CB  LEU A 455 "
       pdb=" CG  LEU A 455 "
    ideal  model  delta    sigma   weight residual
    1.530  1.479  0.051 2.00e-02 2.50e+03 6.51e+00
  bond pdb=" CD  GLU H   6 "
       pdb=" OE2 GLU H   6 "
    ideal  model  delta    sigma   weight residual
    1.249  1.201  0.048 1.90e-02 2.77e+03 6.40e+00
  ... (remaining 5322 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 6105
        1.55 -     3.10: 917
        3.10 -     4.66: 155
        4.66 -     6.21: 41
        6.21 -     7.76: 10
  Bond angle restraints: 7228
  Sorted by residual:
  angle pdb=" C   GLN L  42 "
        pdb=" N   PRO L  43 "
        pdb=" CA  PRO L  43 "
      ideal   model   delta    sigma   weight residual
     119.66  126.03   -6.37 7.20e-01 1.93e+00 7.82e+01
  angle pdb=" C   GLY C   8 "
        pdb=" N   PRO C   9 "
        pdb=" CA  PRO C   9 "
      ideal   model   delta    sigma   weight residual
     119.78  127.54   -7.76 1.03e+00 9.43e-01 5.68e+01
  angle pdb=" C   GLY H 104 "
        pdb=" N   PRO H 105 "
        pdb=" CA  PRO H 105 "
      ideal   model   delta    sigma   weight residual
     119.56  126.58   -7.02 1.01e+00 9.80e-01 4.83e+01
  angle pdb=" C   ILE B  58 "
        pdb=" N   PRO B  59 "
        pdb=" CA  PRO B  59 "
      ideal   model   delta    sigma   weight residual
     119.78  126.73   -6.95 1.03e+00 9.43e-01 4.55e+01
  angle pdb=" C   SER A 383 "
        pdb=" N   PRO A 384 "
        pdb=" CA  PRO A 384 "
      ideal   model   delta    sigma   weight residual
     119.47  127.11   -7.64 1.16e+00 7.43e-01 4.34e+01
  ... (remaining 7223 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.62: 3013
       16.62 -    33.25: 85
       33.25 -    49.87: 24
       49.87 -    66.49: 18
       66.49 -    83.11: 8
  Dihedral angle restraints: 3148
    sinusoidal: 1232
      harmonic: 1916
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.82  -52.82     1      1.00e+01 1.00e-02 3.80e+01
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  92 "
           pdb=" CB  CYS C  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   56.71   36.29     1      1.00e+01 1.00e-02 1.86e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  125.01  -32.01     1      1.00e+01 1.00e-02 1.46e+01
  ... (remaining 3145 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 421
       0.037 -    0.075: 238
       0.075 -    0.112: 88
       0.112 -    0.150: 24
       0.150 -    0.187: 9
  Chirality restraints: 780
  Sorted by residual:
  chirality pdb=" CA  VAL C  37 "
            pdb=" N   VAL C  37 "
            pdb=" C   VAL C  37 "
            pdb=" CB  VAL C  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.73e-01
  chirality pdb=" CA  ILE L  75 "
            pdb=" N   ILE L  75 "
            pdb=" C   ILE L  75 "
            pdb=" CB  ILE L  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.70e-01
  chirality pdb=" CA  TYR A 421 "
            pdb=" N   TYR A 421 "
            pdb=" C   TYR A 421 "
            pdb=" CB  TYR A 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.17e-01
  ... (remaining 777 not shown)

  Planarity restraints: 928
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 489 "    0.030 2.00e-02 2.50e+03   1.63e-02 5.34e+00
        pdb=" CG  TYR A 489 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 489 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 489 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 489 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 489 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 489 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 489 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  32 "    0.027 2.00e-02 2.50e+03   1.62e-02 5.27e+00
        pdb=" CG  TYR L  32 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  32 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  32 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  32 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  32 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  32 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR L  32 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 449 "   -0.025 2.00e-02 2.50e+03   1.37e-02 3.74e+00
        pdb=" CG  TYR A 449 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 449 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 449 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 449 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 449 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 449 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 449 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 925 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 157
        2.69 -     3.24: 4892
        3.24 -     3.80: 8245
        3.80 -     4.35: 11033
        4.35 -     4.90: 18057
  Nonbonded interactions: 42384
  Sorted by model distance:
  nonbonded pdb=" N   TYR L  49 "
            pdb=" CD1 TYR L  49 "
     model   vdw
     2.139 3.420
  nonbonded pdb=" O   LYS H 111 "
            pdb=" OH  TYR H 114 "
     model   vdw
     2.458 3.040
  nonbonded pdb=" O   TYR L  30A"
            pdb=" N   SER L  30C"
     model   vdw
     2.487 3.120
  nonbonded pdb=" O   SER L  93 "
            pdb=" OG1 THR L  94 "
     model   vdw
     2.490 3.040
  nonbonded pdb=" OE1 GLU A 340 "
            pdb=" NZ  LYS A 356 "
     model   vdw
     2.498 3.120
  ... (remaining 42379 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.580
  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:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     19.590
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
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      :  0.012   0.085   5335  Z= 0.624
  Angle     :  1.236   7.760   7245  Z= 0.853
  Chirality :  0.054   0.187    780
  Planarity :  0.005   0.027    927
  Dihedral  : 11.021  83.112   1917
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.52 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  1.06 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  2.20 (0.35), residues: 659
  helix: -4.41 (0.31), residues: 33
  sheet:  1.24 (0.31), residues: 256
  loop :  2.53 (0.36), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.005   TRP A 436 
 HIS   0.003   0.001   HIS B  90 
 PHE   0.015   0.004   PHE H  67 
 TYR   0.030   0.005   TYR A 489 
 ARG   0.002   0.000   ARG H  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.06470 (    1)
  link_NAG-ASN         : angle       1.49950 (    3)
  hydrogen bonds       : bond        0.18854 (  189)
  hydrogen bonds       : angle       8.72196 (  456)
  SS BOND              : bond        0.04585 (    7)
  SS BOND              : angle       2.97151 (   14)
  covalent geometry    : bond        0.01151 ( 5327)
  covalent geometry    : angle       1.22975 ( 7228)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 231
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   67 PHE cc_start: 0.6548 (m-80) cc_final: 0.5847 (m-80)
REVERT: H  120 LEU cc_start: 0.8426 (tp) cc_final: 0.7602 (pp)
REVERT: L    3 VAL cc_start: 0.8346 (t) cc_final: 0.8091 (m)
REVERT: L   46 LEU cc_start: 0.8987 (tp) cc_final: 0.8671 (tp)
REVERT: L   72 THR cc_start: 0.7216 (m) cc_final: 0.6987 (m)
REVERT: L   78 LEU cc_start: 0.8328 (tp) cc_final: 0.7927 (tp)
REVERT: L   85 ILE cc_start: 0.8790 (mm) cc_final: 0.8154 (tp)
REVERT: A  355 ARG cc_start: 0.7939 (ttt90) cc_final: 0.7329 (ttp-170)
REVERT: A  461 LEU cc_start: 0.8715 (mt) cc_final: 0.8506 (mp)
REVERT: B   14 SER cc_start: 0.8112 (m) cc_final: 0.7637 (t)
REVERT: B   36 TYR cc_start: 0.7400 (m-80) cc_final: 0.6903 (m-80)
REVERT: B   46 LEU cc_start: 0.8577 (tp) cc_final: 0.8179 (tp)
REVERT: B   47 LEU cc_start: 0.7761 (mp) cc_final: 0.7494 (mt)
REVERT: C   18 VAL cc_start: 0.8846 (p) cc_final: 0.8563 (p)
REVERT: C   36 TRP cc_start: 0.8957 (m100) cc_final: 0.8585 (m100)
REVERT: C   46 GLU cc_start: 0.8174 (tt0) cc_final: 0.7843 (tp30)
REVERT: C   51 ILE cc_start: 0.8990 (tt) cc_final: 0.8760 (tt)
REVERT: C   70 THR cc_start: 0.8531 (p) cc_final: 0.8182 (t)
REVERT: C   72 ASP cc_start: 0.8597 (t0) cc_final: 0.7883 (t70)
  outliers start: 3
  outliers final: 2
  residues processed: 233
  average time/residue: 0.2148
  time to fit residues: 60.4439
Evaluate side-chains
  121 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    0.0770
   chunk 49 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    1.1542

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN
B   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.095322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.082050 restraints weight = 17837.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.084395 restraints weight = 10231.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.086028 restraints weight = 6938.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   5335  Z= 0.146
  Angle     :  0.658  10.603   7245  Z= 0.354
  Chirality :  0.048   0.310    780
  Planarity :  0.005   0.040    927
  Dihedral  :  4.992  19.140    759
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.12 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.48 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  1.23 (0.33), residues: 659
  helix: -3.78 (0.60), residues: 33
  sheet:  0.62 (0.32), residues: 238
  loop :  1.63 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H 115 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.022   0.002   PHE C  29 
 TYR   0.018   0.002   TYR L  49 
 ARG   0.008   0.001   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00097 (    1)
  link_NAG-ASN         : angle       2.60435 (    3)
  hydrogen bonds       : bond        0.04546 (  189)
  hydrogen bonds       : angle       6.64968 (  456)
  SS BOND              : bond        0.00282 (    7)
  SS BOND              : angle       1.26958 (   14)
  covalent geometry    : bond        0.00323 ( 5327)
  covalent geometry    : angle       0.65418 ( 7228)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7959 (mmm) cc_final: 0.7644 (mmm)
REVERT: H   39 GLN cc_start: 0.7768 (pp30) cc_final: 0.7345 (pp30)
REVERT: H   43 LYS cc_start: 0.8502 (mptt) cc_final: 0.8271 (mmtm)
REVERT: H   46 GLU cc_start: 0.8258 (tt0) cc_final: 0.7838 (tt0)
REVERT: H  111 LYS cc_start: 0.8076 (mtmm) cc_final: 0.7696 (mttt)
REVERT: H  113 ASP cc_start: 0.7118 (t70) cc_final: 0.6506 (p0)
REVERT: H  120 LEU cc_start: 0.8555 (tp) cc_final: 0.7762 (pp)
REVERT: L    3 VAL cc_start: 0.8221 (t) cc_final: 0.7993 (m)
REVERT: L   15 LEU cc_start: 0.8339 (mt) cc_final: 0.7638 (mt)
REVERT: L   58 VAL cc_start: 0.8466 (t) cc_final: 0.8238 (p)
REVERT: L  103 LYS cc_start: 0.8600 (tttt) cc_final: 0.7998 (tptm)
REVERT: A  355 ARG cc_start: 0.7414 (ttt90) cc_final: 0.7129 (ttp-170)
REVERT: A  402 ILE cc_start: 0.8805 (pt) cc_final: 0.8537 (pt)
REVERT: A  422 ASN cc_start: 0.8906 (m-40) cc_final: 0.8120 (m-40)
REVERT: B   49 TYR cc_start: 0.7482 (p90) cc_final: 0.7253 (p90)
REVERT: B  105 GLU cc_start: 0.4458 (tp30) cc_final: 0.4175 (tp30)
REVERT: C    4 LEU cc_start: 0.8184 (mt) cc_final: 0.7647 (mt)
REVERT: C   18 VAL cc_start: 0.8781 (p) cc_final: 0.8136 (p)
REVERT: C   36 TRP cc_start: 0.8818 (m100) cc_final: 0.8605 (m100)
REVERT: C   46 GLU cc_start: 0.8201 (tt0) cc_final: 0.7790 (tp30)
REVERT: C   70 THR cc_start: 0.8581 (p) cc_final: 0.8261 (t)
REVERT: C   71 ARG cc_start: 0.7716 (pmt-80) cc_final: 0.6996 (pmt-80)
REVERT: C   72 ASP cc_start: 0.8552 (t0) cc_final: 0.7813 (t70)
REVERT: C   73 MET cc_start: 0.6884 (pmm) cc_final: 0.6238 (pmm)
REVERT: C   82 LEU cc_start: 0.7960 (tp) cc_final: 0.7622 (tp)
REVERT: C   91 TYR cc_start: 0.9032 (m-80) cc_final: 0.8777 (m-10)
REVERT: C  104 ASP cc_start: 0.8381 (m-30) cc_final: 0.8161 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1728
  time to fit residues: 39.1216
Evaluate side-chains
  121 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 54 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0170
   chunk 20 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    1.3424

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 ASN
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.094289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.081308 restraints weight = 17959.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.083614 restraints weight = 10315.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.085230 restraints weight = 6895.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.4301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   5335  Z= 0.134
  Angle     :  0.591   8.355   7245  Z= 0.322
  Chirality :  0.046   0.268    780
  Planarity :  0.004   0.040    927
  Dihedral  :  4.589  19.295    759
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.58 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.95 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.33), residues: 659
  helix: -3.63 (0.63), residues: 33
  sheet:  0.48 (0.32), residues: 242
  loop :  1.14 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 353 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.022   0.002   PHE H  67 
 TYR   0.017   0.002   TYR L  49 
 ARG   0.005   0.001   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00123 (    1)
  link_NAG-ASN         : angle       1.32993 (    3)
  hydrogen bonds       : bond        0.03909 (  189)
  hydrogen bonds       : angle       6.16126 (  456)
  SS BOND              : bond        0.00417 (    7)
  SS BOND              : angle       1.74933 (   14)
  covalent geometry    : bond        0.00299 ( 5327)
  covalent geometry    : angle       0.58572 ( 7228)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8099 (mmm) cc_final: 0.7732 (mmm)
REVERT: H   39 GLN cc_start: 0.7857 (pp30) cc_final: 0.7325 (pp30)
REVERT: H   43 LYS cc_start: 0.8528 (mptt) cc_final: 0.8320 (mmtm)
REVERT: H   46 GLU cc_start: 0.8040 (tt0) cc_final: 0.7569 (tt0)
REVERT: H   75 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8365 (mmtt)
REVERT: H  120 LEU cc_start: 0.8679 (tp) cc_final: 0.7932 (pp)
REVERT: L   48 MET cc_start: 0.7346 (tpp) cc_final: 0.6793 (mmm)
REVERT: L   58 VAL cc_start: 0.7906 (t) cc_final: 0.7658 (p)
REVERT: A  355 ARG cc_start: 0.7620 (ttt90) cc_final: 0.7341 (ttp-170)
REVERT: A  357 ARG cc_start: 0.8420 (ttm110) cc_final: 0.8105 (ttm110)
REVERT: A  402 ILE cc_start: 0.8790 (pt) cc_final: 0.8482 (pt)
REVERT: A  455 LEU cc_start: 0.8347 (tp) cc_final: 0.8117 (tp)
REVERT: B   17 GLU cc_start: 0.8559 (mp0) cc_final: 0.8334 (mp0)
REVERT: C   46 GLU cc_start: 0.8186 (tt0) cc_final: 0.7866 (tt0)
REVERT: C   47 TRP cc_start: 0.8502 (t60) cc_final: 0.8225 (t60)
REVERT: C   72 ASP cc_start: 0.8659 (t0) cc_final: 0.7631 (t70)
REVERT: C   82 LEU cc_start: 0.8048 (tp) cc_final: 0.7815 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1815
  time to fit residues: 37.2207
Evaluate side-chains
  109 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 56 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 29 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 52 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 48 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 19 optimal weight:   10.0000
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  90 HIS
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.089178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.076063 restraints weight = 18567.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.078260 restraints weight = 10694.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.079804 restraints weight = 7258.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.4957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064   5335  Z= 0.248
  Angle     :  0.693   8.071   7245  Z= 0.377
  Chirality :  0.048   0.340    780
  Planarity :  0.005   0.049    927
  Dihedral  :  5.063  19.670    759
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.30 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.32), residues: 659
  helix: -3.74 (0.76), residues: 27
  sheet:  0.29 (0.31), residues: 255
  loop :  0.64 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP C  50 
 HIS   0.003   0.002   HIS B  90 
 PHE   0.020   0.002   PHE A 374 
 TYR   0.039   0.003   TYR H  99 
 ARG   0.005   0.001   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00075 (    1)
  link_NAG-ASN         : angle       2.00287 (    3)
  hydrogen bonds       : bond        0.04147 (  189)
  hydrogen bonds       : angle       6.27515 (  456)
  SS BOND              : bond        0.01155 (    7)
  SS BOND              : angle       2.08522 (   14)
  covalent geometry    : bond        0.00552 ( 5327)
  covalent geometry    : angle       0.68633 ( 7228)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8198 (tt0) cc_final: 0.7641 (tt0)
REVERT: L   30 LEU cc_start: 0.8529 (tp) cc_final: 0.8256 (tp)
REVERT: L   30 TYR cc_start: 0.8084 (t80) cc_final: 0.7754 (t80)
REVERT: L   33 LEU cc_start: 0.9157 (tp) cc_final: 0.8921 (tp)
REVERT: A  355 ARG cc_start: 0.7635 (ttt90) cc_final: 0.7182 (ttp-170)
REVERT: A  398 ASP cc_start: 0.8787 (m-30) cc_final: 0.8522 (m-30)
REVERT: A  402 ILE cc_start: 0.8996 (pt) cc_final: 0.8729 (pt)
REVERT: A  455 LEU cc_start: 0.8511 (tp) cc_final: 0.8242 (tp)
REVERT: B   46 LEU cc_start: 0.8485 (tp) cc_final: 0.8266 (tp)
REVERT: C   46 GLU cc_start: 0.8241 (tt0) cc_final: 0.7689 (tt0)
REVERT: C   71 ARG cc_start: 0.7527 (ppt170) cc_final: 0.7177 (ppt170)
REVERT: C   72 ASP cc_start: 0.8570 (t0) cc_final: 0.7325 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1659
  time to fit residues: 30.2925
Evaluate side-chains
  100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 47 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 62 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   chunk 14 optimal weight:   20.0000
   overall best weight:    5.9788

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

Flipped N/Q/H residues before XYZ refinement:
H 117 GLN
B  90 HIS
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.085275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.071952 restraints weight = 18996.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.074029 restraints weight = 11254.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.075428 restraints weight = 7858.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.5771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.057   5335  Z= 0.366
  Angle     :  0.845  12.623   7245  Z= 0.448
  Chirality :  0.052   0.367    780
  Planarity :  0.006   0.054    927
  Dihedral  :  5.971  20.006    759
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.32), residues: 659
  helix: -4.18 (0.56), residues: 27
  sheet:  0.05 (0.32), residues: 247
  loop : -0.11 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B  96 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.022   0.003   PHE A 374 
 TYR   0.065   0.003   TYR H  99 
 ARG   0.006   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00320 (    1)
  link_NAG-ASN         : angle       2.55502 (    3)
  hydrogen bonds       : bond        0.04553 (  189)
  hydrogen bonds       : angle       6.57967 (  456)
  SS BOND              : bond        0.01062 (    7)
  SS BOND              : angle       2.50775 (   14)
  covalent geometry    : bond        0.00810 ( 5327)
  covalent geometry    : angle       0.83695 ( 7228)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   67 PHE cc_start: 0.7152 (m-80) cc_final: 0.6704 (m-80)
REVERT: L   30 TYR cc_start: 0.8438 (t80) cc_final: 0.8125 (t80)
REVERT: L   49 TYR cc_start: 0.7643 (p90) cc_final: 0.7293 (p90)
REVERT: L  103 LYS cc_start: 0.8488 (tttt) cc_final: 0.7825 (tptm)
REVERT: A  355 ARG cc_start: 0.7647 (ttt90) cc_final: 0.7178 (ttp-170)
REVERT: A  398 ASP cc_start: 0.8604 (m-30) cc_final: 0.8400 (m-30)
REVERT: A  402 ILE cc_start: 0.9116 (pt) cc_final: 0.8898 (pt)
REVERT: A  455 LEU cc_start: 0.8644 (tp) cc_final: 0.8284 (tp)
REVERT: B   46 LEU cc_start: 0.8495 (tp) cc_final: 0.8224 (tp)
REVERT: C   44 ARG cc_start: 0.8584 (ptt90) cc_final: 0.8307 (mtm110)
REVERT: C   61 GLN cc_start: 0.9110 (mt0) cc_final: 0.8228 (mp10)
REVERT: C   72 ASP cc_start: 0.8625 (t0) cc_final: 0.7417 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1744
  time to fit residues: 28.4919
Evaluate side-chains
  85 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0970
   chunk 53 optimal weight:   10.0000
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
L  37 GLN
L  89 GLN
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.090210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.076844 restraints weight = 18148.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.079099 restraints weight = 10466.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.080625 restraints weight = 7119.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.5759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5335  Z= 0.126
  Angle     :  0.619  11.203   7245  Z= 0.333
  Chirality :  0.047   0.296    780
  Planarity :  0.004   0.047    927
  Dihedral  :  5.142  22.328    759
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.32), residues: 659
  helix: -4.08 (0.57), residues: 27
  sheet:  0.21 (0.32), residues: 244
  loop :  0.00 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  47 
 HIS   0.001   0.000   HIS B  90 
 PHE   0.019   0.002   PHE B  71 
 TYR   0.029   0.002   TYR H  99 
 ARG   0.006   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00144 (    1)
  link_NAG-ASN         : angle       1.64936 (    3)
  hydrogen bonds       : bond        0.03624 (  189)
  hydrogen bonds       : angle       6.09590 (  456)
  SS BOND              : bond        0.00141 (    7)
  SS BOND              : angle       0.88690 (   14)
  covalent geometry    : bond        0.00279 ( 5327)
  covalent geometry    : angle       0.61757 ( 7228)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   30 TYR cc_start: 0.8389 (t80) cc_final: 0.8076 (t80)
REVERT: L  103 LYS cc_start: 0.8535 (tttt) cc_final: 0.7926 (tptt)
REVERT: A  355 ARG cc_start: 0.7584 (ttt90) cc_final: 0.7099 (ttp-170)
REVERT: A  402 ILE cc_start: 0.8945 (pt) cc_final: 0.8741 (pt)
REVERT: A  455 LEU cc_start: 0.8539 (tp) cc_final: 0.8275 (tt)
REVERT: B   46 LEU cc_start: 0.8322 (tp) cc_final: 0.8098 (tp)
REVERT: B   67 SER cc_start: 0.7844 (p) cc_final: 0.7607 (p)
REVERT: B   71 PHE cc_start: 0.7602 (m-10) cc_final: 0.7128 (m-80)
REVERT: C   44 ARG cc_start: 0.8530 (ptt90) cc_final: 0.8264 (ptt90)
REVERT: C   46 GLU cc_start: 0.8198 (tt0) cc_final: 0.7840 (tt0)
REVERT: C   61 GLN cc_start: 0.9046 (mt0) cc_final: 0.8263 (mp10)
REVERT: C   72 ASP cc_start: 0.8717 (t0) cc_final: 0.7460 (t70)
REVERT: C   86 ASP cc_start: 0.7980 (m-30) cc_final: 0.7692 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1825
  time to fit residues: 31.1525
Evaluate side-chains
  100 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:   20.0000
   chunk 56 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 43 optimal weight:   10.0000
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.088285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.075423 restraints weight = 18550.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.077613 restraints weight = 10736.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.079088 restraints weight = 7341.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.6047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5335  Z= 0.177
  Angle     :  0.637   8.435   7245  Z= 0.347
  Chirality :  0.046   0.201    780
  Planarity :  0.005   0.046    927
  Dihedral  :  5.297  23.024    759
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.32), residues: 659
  helix: -4.01 (0.62), residues: 27
  sheet:  0.16 (0.32), residues: 246
  loop : -0.14 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C  50 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.025   0.002   PHE B  71 
 TYR   0.036   0.002   TYR H  99 
 ARG   0.007   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00046 (    1)
  link_NAG-ASN         : angle       1.78214 (    3)
  hydrogen bonds       : bond        0.03836 (  189)
  hydrogen bonds       : angle       5.96616 (  456)
  SS BOND              : bond        0.00694 (    7)
  SS BOND              : angle       0.84005 (   14)
  covalent geometry    : bond        0.00396 ( 5327)
  covalent geometry    : angle       0.63525 ( 7228)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8031 (tt0) cc_final: 0.7459 (tt0)
REVERT: H   67 PHE cc_start: 0.6629 (m-80) cc_final: 0.5646 (m-80)
REVERT: L   30 TYR cc_start: 0.8441 (t80) cc_final: 0.8011 (t80)
REVERT: L   85 ILE cc_start: 0.8651 (mm) cc_final: 0.7969 (tt)
REVERT: A  402 ILE cc_start: 0.8998 (pt) cc_final: 0.8795 (pt)
REVERT: A  455 LEU cc_start: 0.8645 (tp) cc_final: 0.8399 (tp)
REVERT: B   46 LEU cc_start: 0.8411 (tp) cc_final: 0.8098 (tp)
REVERT: B   67 SER cc_start: 0.7924 (p) cc_final: 0.7680 (p)
REVERT: C   46 GLU cc_start: 0.8118 (tt0) cc_final: 0.7449 (tt0)
REVERT: C   58 ASN cc_start: 0.7093 (m-40) cc_final: 0.6695 (t0)
REVERT: C   61 GLN cc_start: 0.9023 (mt0) cc_final: 0.8377 (mp10)
REVERT: C   71 ARG cc_start: 0.7523 (ppt170) cc_final: 0.7150 (ppt170)
REVERT: C   72 ASP cc_start: 0.8645 (t0) cc_final: 0.7236 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1653
  time to fit residues: 28.0124
Evaluate side-chains
  98 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   chunk 60 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0070
   chunk 59 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    1.4004

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.089514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.076367 restraints weight = 18802.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.078570 restraints weight = 10943.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.080080 restraints weight = 7515.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.6220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5335  Z= 0.131
  Angle     :  0.608   6.836   7245  Z= 0.326
  Chirality :  0.046   0.165    780
  Planarity :  0.004   0.047    927
  Dihedral  :  4.993  21.532    759
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.32), residues: 659
  helix: -3.95 (0.65), residues: 27
  sheet:  0.25 (0.33), residues: 242
  loop : -0.17 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C  50 
 HIS   0.001   0.000   HIS B  90 
 PHE   0.012   0.001   PHE A 400 
 TYR   0.028   0.002   TYR H  99 
 ARG   0.008   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00100 (    1)
  link_NAG-ASN         : angle       1.49150 (    3)
  hydrogen bonds       : bond        0.03493 (  189)
  hydrogen bonds       : angle       5.83688 (  456)
  SS BOND              : bond        0.00644 (    7)
  SS BOND              : angle       0.62515 (   14)
  covalent geometry    : bond        0.00292 ( 5327)
  covalent geometry    : angle       0.60710 ( 7228)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7757 (mpp) cc_final: 0.7533 (mpp)
REVERT: H   46 GLU cc_start: 0.7964 (tt0) cc_final: 0.7423 (tt0)
REVERT: H   67 PHE cc_start: 0.6442 (m-80) cc_final: 0.5621 (m-80)
REVERT: L   30 TYR cc_start: 0.8368 (t80) cc_final: 0.7978 (t80)
REVERT: L   85 ILE cc_start: 0.8601 (mm) cc_final: 0.8041 (tp)
REVERT: L  103 LYS cc_start: 0.8517 (tttt) cc_final: 0.7968 (tptt)
REVERT: A  355 ARG cc_start: 0.7540 (ttt90) cc_final: 0.7205 (ttp-170)
REVERT: A  402 ILE cc_start: 0.8989 (pt) cc_final: 0.8743 (pt)
REVERT: A  455 LEU cc_start: 0.8655 (tp) cc_final: 0.8393 (tp)
REVERT: B   46 LEU cc_start: 0.8248 (tp) cc_final: 0.8039 (tp)
REVERT: C   10 GLU cc_start: 0.7544 (pp20) cc_final: 0.7290 (pp20)
REVERT: C   46 GLU cc_start: 0.8145 (tt0) cc_final: 0.7439 (tt0)
REVERT: C   61 GLN cc_start: 0.8969 (mt0) cc_final: 0.8293 (mp10)
REVERT: C   71 ARG cc_start: 0.7588 (ppt170) cc_final: 0.7194 (ppt170)
REVERT: C   72 ASP cc_start: 0.8642 (t0) cc_final: 0.7435 (t70)
REVERT: C   73 MET cc_start: 0.7094 (pmm) cc_final: 0.6616 (ppp)
REVERT: C   86 ASP cc_start: 0.7742 (m-30) cc_final: 0.7433 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1713
  time to fit residues: 29.2171
Evaluate side-chains
  97 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0870
   chunk 30 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 4 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   overall best weight:    1.9362

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

Flipped N/Q/H residues before XYZ refinement:
C  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.088905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.075922 restraints weight = 18531.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.078082 restraints weight = 10656.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.079565 restraints weight = 7264.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.6296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5335  Z= 0.155
  Angle     :  0.617   6.202   7245  Z= 0.331
  Chirality :  0.045   0.151    780
  Planarity :  0.005   0.050    927
  Dihedral  :  4.958  22.557    759
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.32), residues: 659
  helix: -3.97 (0.67), residues: 27
  sheet:  0.34 (0.34), residues: 234
  loop : -0.31 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  50 
 HIS   0.001   0.001   HIS B  90 
 PHE   0.010   0.001   PHE A 400 
 TYR   0.030   0.002   TYR H  99 
 ARG   0.014   0.001   ARG B  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00021 (    1)
  link_NAG-ASN         : angle       1.55339 (    3)
  hydrogen bonds       : bond        0.03606 (  189)
  hydrogen bonds       : angle       5.78966 (  456)
  SS BOND              : bond        0.00596 (    7)
  SS BOND              : angle       0.67871 (   14)
  covalent geometry    : bond        0.00347 ( 5327)
  covalent geometry    : angle       0.61579 ( 7228)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7819 (mpp) cc_final: 0.7565 (mpp)
REVERT: H   46 GLU cc_start: 0.7865 (tt0) cc_final: 0.7309 (tt0)
REVERT: H   67 PHE cc_start: 0.6471 (m-80) cc_final: 0.5628 (m-80)
REVERT: L   85 ILE cc_start: 0.8648 (mm) cc_final: 0.8108 (tp)
REVERT: L  103 LYS cc_start: 0.8474 (tttt) cc_final: 0.7941 (tptt)
REVERT: A  355 ARG cc_start: 0.7423 (ttt90) cc_final: 0.7169 (ttp-170)
REVERT: A  402 ILE cc_start: 0.8972 (pt) cc_final: 0.8716 (pt)
REVERT: A  455 LEU cc_start: 0.8699 (tp) cc_final: 0.8397 (tp)
REVERT: B   46 LEU cc_start: 0.8372 (tp) cc_final: 0.8084 (tp)
REVERT: C   10 GLU cc_start: 0.7598 (pp20) cc_final: 0.7326 (pp20)
REVERT: C   46 GLU cc_start: 0.7982 (tt0) cc_final: 0.7389 (tt0)
REVERT: C   61 GLN cc_start: 0.8995 (mt0) cc_final: 0.8285 (mp10)
REVERT: C   71 ARG cc_start: 0.7594 (ppt170) cc_final: 0.7201 (ppt170)
REVERT: C   72 ASP cc_start: 0.8761 (t0) cc_final: 0.7575 (t70)
REVERT: C   73 MET cc_start: 0.7111 (pmm) cc_final: 0.6634 (ppp)
REVERT: C   86 ASP cc_start: 0.7721 (m-30) cc_final: 0.7499 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1784
  time to fit residues: 28.9861
Evaluate side-chains
  101 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 46 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    2.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.088567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.075283 restraints weight = 18796.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.077453 restraints weight = 11057.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.078892 restraints weight = 7658.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.6421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5335  Z= 0.194
  Angle     :  0.642   6.168   7245  Z= 0.346
  Chirality :  0.046   0.153    780
  Planarity :  0.005   0.056    927
  Dihedral  :  5.123  21.911    759
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.32), residues: 659
  helix: -3.97 (0.67), residues: 27
  sheet:  0.10 (0.33), residues: 237
  loop : -0.45 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  96 
 HIS   0.005   0.002   HIS B  90 
 PHE   0.013   0.002   PHE H  67 
 TYR   0.034   0.002   TYR H  99 
 ARG   0.011   0.001   ARG B  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00044 (    1)
  link_NAG-ASN         : angle       1.67419 (    3)
  hydrogen bonds       : bond        0.03710 (  189)
  hydrogen bonds       : angle       6.02355 (  456)
  SS BOND              : bond        0.00524 (    7)
  SS BOND              : angle       0.75856 (   14)
  covalent geometry    : bond        0.00431 ( 5327)
  covalent geometry    : angle       0.64060 ( 7228)

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.7944 (tt0) cc_final: 0.7322 (tt0)
REVERT: H   67 PHE cc_start: 0.6508 (m-80) cc_final: 0.5702 (m-80)
REVERT: L  103 LYS cc_start: 0.8447 (tttt) cc_final: 0.7951 (tptt)
REVERT: A  355 ARG cc_start: 0.7474 (ttt90) cc_final: 0.7180 (ttp-170)
REVERT: A  402 ILE cc_start: 0.9012 (pt) cc_final: 0.8766 (pt)
REVERT: A  455 LEU cc_start: 0.8741 (tp) cc_final: 0.8422 (tp)
REVERT: A  464 PHE cc_start: 0.8379 (m-80) cc_final: 0.8037 (m-80)
REVERT: B   46 LEU cc_start: 0.8400 (tp) cc_final: 0.8198 (tp)
REVERT: C   10 GLU cc_start: 0.7658 (pp20) cc_final: 0.7309 (pp20)
REVERT: C   46 GLU cc_start: 0.8035 (tt0) cc_final: 0.7603 (tt0)
REVERT: C   72 ASP cc_start: 0.8807 (t0) cc_final: 0.7558 (t70)
REVERT: C   86 ASP cc_start: 0.7886 (m-30) cc_final: 0.7501 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1843
  time to fit residues: 30.0106
Evaluate side-chains
  91 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 12 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0870
   chunk 24 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 63 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
L  30EASN
B  90 HIS
C  58 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.090651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.077625 restraints weight = 18635.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.079823 restraints weight = 10846.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.081364 restraints weight = 7405.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.6497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5335  Z= 0.116
  Angle     :  0.607   7.423   7245  Z= 0.320
  Chirality :  0.045   0.159    780
  Planarity :  0.004   0.052    927
  Dihedral  :  4.813  20.960    759
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.32), residues: 659
  helix: -3.92 (0.65), residues: 27
  sheet:  0.15 (0.33), residues: 237
  loop : -0.35 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  47 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.012   0.001   PHE A 400 
 TYR   0.024   0.002   TYR H  99 
 ARG   0.014   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00150 (    1)
  link_NAG-ASN         : angle       1.33962 (    3)
  hydrogen bonds       : bond        0.03544 (  189)
  hydrogen bonds       : angle       5.72144 (  456)
  SS BOND              : bond        0.00574 (    7)
  SS BOND              : angle       0.76424 (   14)
  covalent geometry    : bond        0.00254 ( 5327)
  covalent geometry    : angle       0.60636 ( 7228)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2243.21 seconds
wall clock time: 39 minutes 32.41 seconds (2372.41 seconds total)