Starting phenix.real_space_refine
on Sat May 10 06:04:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d8q_27254/05_2025/8d8q_27254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d8q_27254/05_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_27254/05_2025/8d8q_27254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d8q_27254/05_2025/8d8q_27254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d8q_27254/05_2025/8d8q_27254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d8q_27254/05_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-5687/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: 5.00, per 1000 atoms: 0.96
  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: 1.33
  Conformation dependent library (CDL) restraints added in 652.2 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: 0.83
  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: 1.57

  Time building geometry restraints manager: 1.55 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:             9.980
  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:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     17.780
  Find NCS groups from input model:        0.070
  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:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.710
-------------------------------------------------------------------------------
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  : 0.603 
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: 0.2100
  time to fit residues: 59.0602
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  : 0.547 
-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.095188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.081971 restraints weight = 17706.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.084351 restraints weight = 10092.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.085976 restraints weight = 6796.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
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  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7958 (mmm) cc_final: 0.7643 (mmm)
REVERT: H   39 GLN cc_start: 0.7772 (pp30) cc_final: 0.7347 (pp30)
REVERT: H   43 LYS cc_start: 0.8503 (mptt) cc_final: 0.8271 (mmtm)
REVERT: H   46 GLU cc_start: 0.8261 (tt0) cc_final: 0.7837 (tt0)
REVERT: H  111 LYS cc_start: 0.8073 (mtmm) cc_final: 0.7693 (mttt)
REVERT: H  113 ASP cc_start: 0.7117 (t70) cc_final: 0.6507 (p0)
REVERT: H  120 LEU cc_start: 0.8555 (tp) cc_final: 0.7762 (pp)
REVERT: L    3 VAL cc_start: 0.8222 (t) cc_final: 0.7994 (m)
REVERT: L   15 LEU cc_start: 0.8337 (mt) cc_final: 0.7637 (mt)
REVERT: L   58 VAL cc_start: 0.8463 (t) cc_final: 0.8236 (p)
REVERT: L  103 LYS cc_start: 0.8601 (tttt) cc_final: 0.7998 (tptm)
REVERT: A  355 ARG cc_start: 0.7411 (ttt90) cc_final: 0.7127 (ttp-170)
REVERT: A  402 ILE cc_start: 0.8806 (pt) cc_final: 0.8537 (pt)
REVERT: A  422 ASN cc_start: 0.8902 (m-40) cc_final: 0.8117 (m-40)
REVERT: B   49 TYR cc_start: 0.7482 (p90) cc_final: 0.7253 (p90)
REVERT: B  105 GLU cc_start: 0.4456 (tp30) cc_final: 0.4176 (tp30)
REVERT: C    4 LEU cc_start: 0.8188 (mt) cc_final: 0.7650 (mt)
REVERT: C   18 VAL cc_start: 0.8783 (p) cc_final: 0.8137 (p)
REVERT: C   36 TRP cc_start: 0.8818 (m100) cc_final: 0.8601 (m100)
REVERT: C   46 GLU cc_start: 0.8204 (tt0) cc_final: 0.7788 (tp30)
REVERT: C   70 THR cc_start: 0.8582 (p) cc_final: 0.8261 (t)
REVERT: C   71 ARG cc_start: 0.7718 (pmt-80) cc_final: 0.6998 (pmt-80)
REVERT: C   72 ASP cc_start: 0.8552 (t0) cc_final: 0.7812 (t70)
REVERT: C   73 MET cc_start: 0.6887 (pmm) cc_final: 0.6239 (pmm)
REVERT: C   82 LEU cc_start: 0.7961 (tp) cc_final: 0.7623 (tp)
REVERT: C   91 TYR cc_start: 0.9035 (m-80) cc_final: 0.8776 (m-10)
REVERT: C  104 ASP cc_start: 0.8383 (m-30) cc_final: 0.8165 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1845
  time to fit residues: 41.9343
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  : 0.621 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 48 optimal weight:    0.3980
   chunk 20 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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  30EASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.095397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.082430 restraints weight = 17813.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.084791 restraints weight = 10118.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.086438 restraints weight = 6722.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5335  Z= 0.123
  Angle     :  0.587   7.721   7245  Z= 0.319
  Chirality :  0.046   0.268    780
  Planarity :  0.004   0.041    927
  Dihedral  :  4.578  19.078    759
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.43 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.77 %
    Favored  : 98.05 %
  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:  0.80 (0.33), residues: 659
  helix: -3.63 (0.64), residues: 33
  sheet:  0.48 (0.32), residues: 242
  loop :  1.18 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 353 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.027   0.002   PHE H  67 
 TYR   0.018   0.001   TYR L  91 
 ARG   0.006   0.001   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00124 (    1)
  link_NAG-ASN         : angle       1.37825 (    3)
  hydrogen bonds       : bond        0.03897 (  189)
  hydrogen bonds       : angle       6.22725 (  456)
  SS BOND              : bond        0.01103 (    7)
  SS BOND              : angle       1.64700 (   14)
  covalent geometry    : bond        0.00270 ( 5327)
  covalent geometry    : angle       0.58248 ( 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
  163 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8110 (mmm) cc_final: 0.7713 (mmm)
REVERT: H   39 GLN cc_start: 0.7924 (pp30) cc_final: 0.7394 (pp30)
REVERT: H   43 LYS cc_start: 0.8500 (mptt) cc_final: 0.8292 (mmtm)
REVERT: H   46 GLU cc_start: 0.8114 (tt0) cc_final: 0.7667 (tt0)
REVERT: H   75 LYS cc_start: 0.8727 (mmmm) cc_final: 0.8350 (mmtt)
REVERT: H  120 LEU cc_start: 0.8609 (tp) cc_final: 0.7901 (pp)
REVERT: L   48 MET cc_start: 0.7274 (tpp) cc_final: 0.6696 (mmm)
REVERT: L   58 VAL cc_start: 0.7819 (t) cc_final: 0.7570 (p)
REVERT: A  355 ARG cc_start: 0.7586 (ttt90) cc_final: 0.7285 (ttp-170)
REVERT: A  357 ARG cc_start: 0.8427 (ttm110) cc_final: 0.7828 (ttm170)
REVERT: A  398 ASP cc_start: 0.8550 (m-30) cc_final: 0.8342 (m-30)
REVERT: A  402 ILE cc_start: 0.8760 (pt) cc_final: 0.8437 (pt)
REVERT: B   17 GLU cc_start: 0.8532 (mp0) cc_final: 0.8302 (mp0)
REVERT: C   46 GLU cc_start: 0.8281 (tt0) cc_final: 0.7895 (tt0)
REVERT: C   47 TRP cc_start: 0.8433 (t60) cc_final: 0.8117 (t60)
REVERT: C   70 THR cc_start: 0.8584 (p) cc_final: 0.8303 (t)
REVERT: C   72 ASP cc_start: 0.8644 (t0) cc_final: 0.7640 (t70)
REVERT: C   82 LEU cc_start: 0.8025 (tp) cc_final: 0.7776 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 163
  average time/residue: 0.1767
  time to fit residues: 36.2677
Evaluate side-chains
  106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 29 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 52 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 48 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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 = 0.3557 r_free = 0.3557 target = 0.091841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.078605 restraints weight = 18439.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.080866 restraints weight = 10421.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.082447 restraints weight = 7044.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.4770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   5335  Z= 0.183
  Angle     :  0.628   8.399   7245  Z= 0.343
  Chirality :  0.047   0.341    780
  Planarity :  0.005   0.039    927
  Dihedral  :  4.760  20.751    759
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  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:  0.44 (0.32), residues: 659
  helix: -3.65 (0.74), residues: 27
  sheet:  0.32 (0.31), residues: 250
  loop :  0.75 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  50 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.025   0.002   PHE A 374 
 TYR   0.030   0.002   TYR H  99 
 ARG   0.005   0.001   ARG C  71 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00009 (    1)
  link_NAG-ASN         : angle       1.65525 (    3)
  hydrogen bonds       : bond        0.03821 (  189)
  hydrogen bonds       : angle       6.13129 (  456)
  SS BOND              : bond        0.00780 (    7)
  SS BOND              : angle       1.85873 (   14)
  covalent geometry    : bond        0.00407 ( 5327)
  covalent geometry    : angle       0.62284 ( 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
  146 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8098 (mmm) cc_final: 0.7729 (mmm)
REVERT: H   39 GLN cc_start: 0.7803 (pp30) cc_final: 0.7029 (pp30)
REVERT: H   43 LYS cc_start: 0.8469 (mptt) cc_final: 0.8255 (mmtm)
REVERT: H   46 GLU cc_start: 0.8155 (tt0) cc_final: 0.7598 (tt0)
REVERT: L   30 LEU cc_start: 0.8473 (tp) cc_final: 0.8137 (tp)
REVERT: L   30 TYR cc_start: 0.8219 (t80) cc_final: 0.7518 (t80)
REVERT: L   33 LEU cc_start: 0.9037 (tp) cc_final: 0.8770 (tt)
REVERT: A  340 GLU cc_start: 0.8578 (mp0) cc_final: 0.8353 (tp30)
REVERT: A  355 ARG cc_start: 0.7642 (ttt90) cc_final: 0.7194 (ttp-170)
REVERT: A  398 ASP cc_start: 0.8796 (m-30) cc_final: 0.8574 (m-30)
REVERT: A  402 ILE cc_start: 0.8912 (pt) cc_final: 0.8650 (pt)
REVERT: A  455 LEU cc_start: 0.8465 (tp) cc_final: 0.8231 (tp)
REVERT: B   46 LEU cc_start: 0.8509 (tp) cc_final: 0.8260 (tp)
REVERT: C   46 GLU cc_start: 0.8248 (tt0) cc_final: 0.7727 (tt0)
REVERT: C   47 TRP cc_start: 0.8665 (t60) cc_final: 0.8355 (t60)
REVERT: C   71 ARG cc_start: 0.7437 (ppt170) cc_final: 0.7030 (ppt170)
REVERT: C   72 ASP cc_start: 0.8556 (t0) cc_final: 0.7404 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1817
  time to fit residues: 34.1702
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  : 0.670 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 62 optimal weight:   20.0000
   chunk 35 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 14 optimal weight:   20.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
H 117 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3449 r_free = 0.3449 target = 0.086640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.073185 restraints weight = 18849.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.075326 restraints weight = 11258.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.076788 restraints weight = 7867.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.5549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   5335  Z= 0.305
  Angle     :  0.773  12.463   7245  Z= 0.415
  Chirality :  0.050   0.351    780
  Planarity :  0.005   0.047    927
  Dihedral  :  5.597  19.978    759
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    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: -0.12 (0.32), residues: 659
  helix: -3.88 (0.68), residues: 27
  sheet:  0.20 (0.33), residues: 240
  loop :  0.14 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP B  96 
 HIS   0.004   0.002   HIS B  90 
 PHE   0.023   0.003   PHE A 515 
 TYR   0.042   0.003   TYR H  99 
 ARG   0.007   0.001   ARG H  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00122 (    1)
  link_NAG-ASN         : angle       2.32118 (    3)
  hydrogen bonds       : bond        0.04279 (  189)
  hydrogen bonds       : angle       6.36773 (  456)
  SS BOND              : bond        0.00992 (    7)
  SS BOND              : angle       1.94254 (   14)
  covalent geometry    : bond        0.00673 ( 5327)
  covalent geometry    : angle       0.76800 ( 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
  132 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   67 PHE cc_start: 0.7219 (m-80) cc_final: 0.6832 (m-80)
REVERT: A  340 GLU cc_start: 0.8564 (mp0) cc_final: 0.8315 (tp30)
REVERT: A  402 ILE cc_start: 0.9067 (pt) cc_final: 0.8820 (pt)
REVERT: A  410 ILE cc_start: 0.9215 (mm) cc_final: 0.9006 (mm)
REVERT: A  455 LEU cc_start: 0.8525 (tp) cc_final: 0.8218 (tp)
REVERT: B   46 LEU cc_start: 0.8463 (tp) cc_final: 0.8156 (tp)
REVERT: C   10 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6981 (tm-30)
REVERT: C   46 GLU cc_start: 0.8192 (tt0) cc_final: 0.7789 (tt0)
REVERT: C   61 GLN cc_start: 0.9030 (mt0) cc_final: 0.8218 (mp10)
REVERT: C   71 ARG cc_start: 0.7674 (ppt170) cc_final: 0.7414 (ppt170)
REVERT: C   72 ASP cc_start: 0.8624 (t0) cc_final: 0.7410 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1729
  time to fit residues: 29.6292
Evaluate side-chains
  87 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 37 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 53 optimal weight:   10.0000
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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**
B  90 HIS
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.091454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.078050 restraints weight = 18188.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.080251 restraints weight = 10620.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.081823 restraints weight = 7323.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.5660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5335  Z= 0.129
  Angle     :  0.619   9.855   7245  Z= 0.335
  Chirality :  0.046   0.226    780
  Planarity :  0.004   0.047    927
  Dihedral  :  4.952  21.471    759
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  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: -0.15 (0.32), residues: 659
  helix: -3.85 (0.64), residues: 27
  sheet:  0.36 (0.33), residues: 233
  loop : -0.02 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  47 
 HIS   0.003   0.001   HIS B  90 
 PHE   0.012   0.001   PHE A 400 
 TYR   0.027   0.001   TYR H  99 
 ARG   0.010   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00236 (    1)
  link_NAG-ASN         : angle       1.48452 (    3)
  hydrogen bonds       : bond        0.03488 (  189)
  hydrogen bonds       : angle       6.08817 (  456)
  SS BOND              : bond        0.00880 (    7)
  SS BOND              : angle       0.84325 (   14)
  covalent geometry    : bond        0.00285 ( 5327)
  covalent geometry    : angle       0.61780 ( 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  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8039 (mmm) cc_final: 0.7706 (mmm)
REVERT: H   46 GLU cc_start: 0.8042 (tt0) cc_final: 0.7417 (tt0)
REVERT: L   33 LEU cc_start: 0.9113 (tp) cc_final: 0.8906 (tp)
REVERT: A  378 LYS cc_start: 0.8729 (tptp) cc_final: 0.8253 (tptp)
REVERT: A  402 ILE cc_start: 0.8932 (pt) cc_final: 0.8681 (pt)
REVERT: A  409 GLN cc_start: 0.8536 (mp10) cc_final: 0.8095 (mp10)
REVERT: A  455 LEU cc_start: 0.8518 (tp) cc_final: 0.8255 (tp)
REVERT: B   36 TYR cc_start: 0.8665 (m-80) cc_final: 0.8392 (m-10)
REVERT: B   79 GLU cc_start: 0.7511 (mp0) cc_final: 0.7293 (mp0)
REVERT: C   44 ARG cc_start: 0.8554 (ptt90) cc_final: 0.8229 (ptt90)
REVERT: C   46 GLU cc_start: 0.8283 (tt0) cc_final: 0.7866 (tt0)
REVERT: C   72 ASP cc_start: 0.8708 (t0) cc_final: 0.7438 (t70)
REVERT: C   86 ASP cc_start: 0.7680 (m-30) cc_final: 0.7385 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1930
  time to fit residues: 32.7400
Evaluate side-chains
  95 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 7 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 49 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 1 optimal weight:    0.2980
   chunk 14 optimal weight:   30.0000
   chunk 56 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 43 optimal weight:    9.9990
   overall best weight:    2.2384

-------------------------------------------------------------------------------
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**
** B  89 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 = 0.3514 r_free = 0.3514 target = 0.089647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.076269 restraints weight = 18204.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.078416 restraints weight = 10664.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.079900 restraints weight = 7360.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.5930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5335  Z= 0.173
  Angle     :  0.633   7.437   7245  Z= 0.342
  Chirality :  0.047   0.243    780
  Planarity :  0.005   0.046    927
  Dihedral  :  4.960  20.202    759
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  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: -0.17 (0.32), residues: 659
  helix: -3.85 (0.61), residues: 27
  sheet:  0.30 (0.34), residues: 235
  loop :  0.00 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 353 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.021   0.002   PHE B  71 
 TYR   0.027   0.002   TYR H  99 
 ARG   0.009   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00011 (    1)
  link_NAG-ASN         : angle       1.74998 (    3)
  hydrogen bonds       : bond        0.03760 (  189)
  hydrogen bonds       : angle       5.89521 (  456)
  SS BOND              : bond        0.00749 (    7)
  SS BOND              : angle       0.68852 (   14)
  covalent geometry    : bond        0.00388 ( 5327)
  covalent geometry    : angle       0.63208 ( 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
  125 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  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: 0.8021 (mmm) cc_final: 0.7639 (mmm)
REVERT: H   46 GLU cc_start: 0.8036 (tt0) cc_final: 0.7436 (tt0)
REVERT: H   67 PHE cc_start: 0.6607 (m-80) cc_final: 0.5903 (m-80)
REVERT: L   85 ILE cc_start: 0.8613 (mm) cc_final: 0.8108 (tp)
REVERT: A  402 ILE cc_start: 0.8979 (pt) cc_final: 0.8739 (pt)
REVERT: A  455 LEU cc_start: 0.8615 (tp) cc_final: 0.8406 (tp)
REVERT: A  464 PHE cc_start: 0.8335 (m-80) cc_final: 0.8111 (m-80)
REVERT: B   46 LEU cc_start: 0.8402 (tp) cc_final: 0.8043 (tp)
REVERT: B   71 PHE cc_start: 0.7695 (m-10) cc_final: 0.7330 (m-80)
REVERT: C   46 GLU cc_start: 0.8087 (tt0) cc_final: 0.7468 (tt0)
REVERT: C   58 ASN cc_start: 0.7349 (m-40) cc_final: 0.7117 (t0)
REVERT: C   72 ASP cc_start: 0.8686 (t0) cc_final: 0.7425 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1809
  time to fit residues: 28.7863
Evaluate side-chains
  92 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0970
   chunk 3 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    2.0186

-------------------------------------------------------------------------------
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 = 0.3509 r_free = 0.3509 target = 0.089243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.075838 restraints weight = 18559.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.077996 restraints weight = 10868.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.079491 restraints weight = 7509.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.6145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5335  Z= 0.155
  Angle     :  0.629   6.389   7245  Z= 0.335
  Chirality :  0.046   0.193    780
  Planarity :  0.004   0.046    927
  Dihedral  :  4.943  19.824    759
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  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: -0.22 (0.32), residues: 659
  helix: -3.72 (0.69), residues: 27
  sheet:  0.31 (0.33), residues: 239
  loop : -0.08 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  96 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.019   0.001   PHE B  71 
 TYR   0.025   0.002   TYR H  99 
 ARG   0.014   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00064 (    1)
  link_NAG-ASN         : angle       1.62499 (    3)
  hydrogen bonds       : bond        0.03536 (  189)
  hydrogen bonds       : angle       5.79405 (  456)
  SS BOND              : bond        0.00585 (    7)
  SS BOND              : angle       0.69024 (   14)
  covalent geometry    : bond        0.00350 ( 5327)
  covalent geometry    : angle       0.62778 ( 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
  125 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8024 (mmm) cc_final: 0.7699 (mpp)
REVERT: H   46 GLU cc_start: 0.7987 (tt0) cc_final: 0.7408 (tt0)
REVERT: H   67 PHE cc_start: 0.6415 (m-80) cc_final: 0.5877 (m-80)
REVERT: L   85 ILE cc_start: 0.8636 (mm) cc_final: 0.8122 (tp)
REVERT: A  402 ILE cc_start: 0.8976 (pt) cc_final: 0.8707 (pt)
REVERT: A  455 LEU cc_start: 0.8732 (tp) cc_final: 0.8475 (tp)
REVERT: B   46 LEU cc_start: 0.8238 (tp) cc_final: 0.8001 (tp)
REVERT: C   44 ARG cc_start: 0.8528 (ptt90) cc_final: 0.8249 (ptt90)
REVERT: C   46 GLU cc_start: 0.8125 (tt0) cc_final: 0.7627 (tt0)
REVERT: C   58 ASN cc_start: 0.7251 (m-40) cc_final: 0.6950 (t0)
REVERT: C   72 ASP cc_start: 0.8667 (t0) cc_final: 0.7816 (t70)
REVERT: C   73 MET cc_start: 0.7108 (pmm) cc_final: 0.6564 (ppp)
REVERT: C   82 LEU cc_start: 0.8161 (tp) cc_final: 0.7957 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1772
  time to fit residues: 28.2422
Evaluate side-chains
  93 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 19 optimal weight:   10.0000
   overall best weight:    1.5582

-------------------------------------------------------------------------------
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 = 0.3510 r_free = 0.3510 target = 0.089529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.076069 restraints weight = 18779.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.078187 restraints weight = 11153.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.079662 restraints weight = 7784.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.6249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5335  Z= 0.140
  Angle     :  0.622   6.826   7245  Z= 0.332
  Chirality :  0.045   0.172    780
  Planarity :  0.005   0.052    927
  Dihedral  :  4.875  23.208    759
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  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: -0.23 (0.32), residues: 659
  helix: -3.68 (0.72), residues: 27
  sheet:  0.38 (0.34), residues: 239
  loop : -0.15 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.001   0.001   HIS B  90 
 PHE   0.009   0.001   PHE H 112 
 TYR   0.022   0.002   TYR H  99 
 ARG   0.014   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00060 (    1)
  link_NAG-ASN         : angle       1.55614 (    3)
  hydrogen bonds       : bond        0.03640 (  189)
  hydrogen bonds       : angle       5.82001 (  456)
  SS BOND              : bond        0.00675 (    7)
  SS BOND              : angle       0.88066 (   14)
  covalent geometry    : bond        0.00313 ( 5327)
  covalent geometry    : angle       0.62055 ( 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
  120 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8032 (mmm) cc_final: 0.7648 (mmm)
REVERT: H   46 GLU cc_start: 0.7806 (tt0) cc_final: 0.7164 (tt0)
REVERT: H   67 PHE cc_start: 0.6368 (m-80) cc_final: 0.5894 (m-80)
REVERT: L   85 ILE cc_start: 0.8601 (mm) cc_final: 0.8137 (tp)
REVERT: A  402 ILE cc_start: 0.8939 (pt) cc_final: 0.8673 (pt)
REVERT: A  455 LEU cc_start: 0.8663 (tp) cc_final: 0.8410 (tp)
REVERT: B   46 LEU cc_start: 0.8283 (tp) cc_final: 0.7916 (tp)
REVERT: C   46 GLU cc_start: 0.8198 (tt0) cc_final: 0.7647 (tt0)
REVERT: C   57 THR cc_start: 0.8611 (p) cc_final: 0.8388 (p)
REVERT: C   72 ASP cc_start: 0.8600 (t0) cc_final: 0.7961 (t70)
REVERT: C   73 MET cc_start: 0.7107 (pmm) cc_final: 0.6616 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1821
  time to fit residues: 27.6854
Evaluate side-chains
  93 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 46 optimal weight:    7.9990
   chunk 24 optimal weight:    0.4980
   chunk 20 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 30 optimal weight:    9.9990
   chunk 62 optimal weight:   20.0000
   chunk 27 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 38 optimal weight:    0.4980
   overall best weight:    2.1584

-------------------------------------------------------------------------------
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 = 0.3505 r_free = 0.3505 target = 0.089206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.075847 restraints weight = 18927.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.077924 restraints weight = 11358.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.079377 restraints weight = 7940.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.6442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5335  Z= 0.162
  Angle     :  0.629   6.010   7245  Z= 0.338
  Chirality :  0.046   0.167    780
  Planarity :  0.005   0.057    927
  Dihedral  :  4.892  23.552    759
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  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: -0.33 (0.32), residues: 659
  helix: -3.63 (0.76), residues: 27
  sheet:  0.33 (0.34), residues: 239
  loop : -0.25 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 436 
 HIS   0.003   0.001   HIS B  90 
 PHE   0.022   0.002   PHE B  71 
 TYR   0.022   0.002   TYR H  99 
 ARG   0.014   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00017 (    1)
  link_NAG-ASN         : angle       1.59629 (    3)
  hydrogen bonds       : bond        0.03629 (  189)
  hydrogen bonds       : angle       5.87493 (  456)
  SS BOND              : bond        0.00553 (    7)
  SS BOND              : angle       0.73933 (   14)
  covalent geometry    : bond        0.00365 ( 5327)
  covalent geometry    : angle       0.62788 ( 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
  114 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8036 (mmm) cc_final: 0.7771 (mpp)
REVERT: H   46 GLU cc_start: 0.7850 (tt0) cc_final: 0.7201 (tt0)
REVERT: H   67 PHE cc_start: 0.6278 (m-80) cc_final: 0.5624 (m-80)
REVERT: H   73 ASP cc_start: 0.8427 (m-30) cc_final: 0.8154 (m-30)
REVERT: L   85 ILE cc_start: 0.8658 (mm) cc_final: 0.8152 (tp)
REVERT: A  402 ILE cc_start: 0.8986 (pt) cc_final: 0.8738 (pt)
REVERT: A  455 LEU cc_start: 0.8724 (tp) cc_final: 0.8452 (tp)
REVERT: B   46 LEU cc_start: 0.8166 (tp) cc_final: 0.7937 (tp)
REVERT: C   46 GLU cc_start: 0.7972 (tt0) cc_final: 0.7562 (tt0)
REVERT: C   72 ASP cc_start: 0.8637 (t0) cc_final: 0.8003 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1729
  time to fit residues: 25.5055
Evaluate side-chains
  92 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 34 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 24 optimal weight:    0.5980
   chunk 9 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** L  30DASN ** 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 = 0.3537 r_free = 0.3537 target = 0.090701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.077184 restraints weight = 18921.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.079282 restraints weight = 11358.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.080765 restraints weight = 7943.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.6516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5335  Z= 0.123
  Angle     :  0.593   5.875   7245  Z= 0.315
  Chirality :  0.045   0.193    780
  Planarity :  0.005   0.055    927
  Dihedral  :  4.693  23.365    759
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  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: -0.27 (0.33), residues: 659
  helix: -3.61 (0.77), residues: 27
  sheet:  0.32 (0.34), residues: 235
  loop : -0.16 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  50 
 HIS   0.001   0.000   HIS B  90 
 PHE   0.015   0.001   PHE A 464 
 TYR   0.020   0.002   TYR H  99 
 ARG   0.015   0.001   ARG A 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00095 (    1)
  link_NAG-ASN         : angle       1.44705 (    3)
  hydrogen bonds       : bond        0.03495 (  189)
  hydrogen bonds       : angle       5.73747 (  456)
  SS BOND              : bond        0.00560 (    7)
  SS BOND              : angle       0.69798 (   14)
  covalent geometry    : bond        0.00275 ( 5327)
  covalent geometry    : angle       0.59216 ( 7228)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2138.71 seconds
wall clock time: 38 minutes 32.86 seconds (2312.86 seconds total)